diff --git a/v03_pipeline/bin/pipeline_worker.py b/v03_pipeline/bin/pipeline_worker.py index 7ed39774d..ecf214815 100755 --- a/v03_pipeline/bin/pipeline_worker.py +++ b/v03_pipeline/bin/pipeline_worker.py @@ -13,7 +13,6 @@ project_remap_path, ) from v03_pipeline.lib.tasks import ( - UpdateCachedReferenceDatasetQueries, UpdateVariantAnnotationsTableWithNewSamplesTask, WriteProjectFamilyTablesTask, ) @@ -50,10 +49,6 @@ def main(): k: v for k, v in lpr.model_dump().items() if k != 'projects_to_run' } tasks = [ - UpdateCachedReferenceDatasetQueries( - reference_genome=lpr.reference_genome, - dataset_type=lpr.dataset_type, - ), UpdateVariantAnnotationsTableWithNewSamplesTask( project_guids=lpr.projects_to_run, project_remap_paths=project_remap_paths, diff --git a/v03_pipeline/lib/misc/io.py b/v03_pipeline/lib/misc/io.py index bea1b9bc5..5c82fabe7 100644 --- a/v03_pipeline/lib/misc/io.py +++ b/v03_pipeline/lib/misc/io.py @@ -80,6 +80,7 @@ def compute_hail_n_partitions(file_size_b: int) -> int: ) def split_multi_hts( mt: hl.MatrixTable, + skip_validation: bool, max_samples_split_multi_shuffle=MAX_SAMPLES_SPLIT_MULTI_SHUFFLE, ) -> hl.MatrixTable: bi = mt.filter_rows(hl.len(mt.alleles) == BIALLELIC) @@ -94,7 +95,11 @@ def split_multi_hts( permit_shuffle=mt.count()[1] < max_samples_split_multi_shuffle, ) mt = split.union_rows(bi) - return mt.distinct_by_row() + # If we've disabled validation (which is expected to throw an exception + # for duplicate variants, we would like to distinc ) + if skip_validation: + return mt.distinct_by_row() + return mt def import_gcnv_bed_file(callset_path: str) -> hl.MatrixTable: diff --git a/v03_pipeline/lib/misc/io_test.py b/v03_pipeline/lib/misc/io_test.py index 24792755a..50f123572 100644 --- a/v03_pipeline/lib/misc/io_test.py +++ b/v03_pipeline/lib/misc/io_test.py @@ -170,5 +170,6 @@ def test_split_multi_failure(self) -> None: ) .key_rows_by('locus', 'alleles') .repartition(1), + False, 1, ) diff --git a/v03_pipeline/lib/misc/validation.py b/v03_pipeline/lib/misc/validation.py index c4374c4be..72fbb5b82 100644 --- a/v03_pipeline/lib/misc/validation.py +++ b/v03_pipeline/lib/misc/validation.py @@ -75,13 +75,17 @@ def validate_allele_type( def validate_no_duplicate_variants( mt: hl.MatrixTable, + reference_genome: ReferenceGenome, + dataset_type: DatasetType, **_: Any, ) -> None: ht = mt.rows() ht = ht.group_by(*ht.key).aggregate(n=hl.agg.count()) ht = ht.filter(ht.n > 1) + ht = ht.select() if ht.count() > 0: - msg = f'Variants are present multiple times in the callset: {ht.collect()}' + variant_format = dataset_type.table_key_format_fn(reference_genome) + msg = f'Variants are present multiple times in the callset: {[variant_format(v) for v in ht.collect()]}' raise SeqrValidationError(msg) @@ -99,7 +103,7 @@ def validate_expected_contig_frequency( ) if missing_contigs: msg = 'Missing the following expected contigs:{}'.format( - ', '.join(missing_contigs), + ', '.join(sorted(missing_contigs)), ) raise SeqrValidationError(msg) diff --git a/v03_pipeline/lib/misc/validation_test.py b/v03_pipeline/lib/misc/validation_test.py index 28c8e8e15..81d1185cf 100644 --- a/v03_pipeline/lib/misc/validation_test.py +++ b/v03_pipeline/lib/misc/validation_test.py @@ -171,15 +171,22 @@ def test_validate_no_duplicate_variants(self) -> None: reference_genome='GRCh38', ), ], + 'alleles': [ + ['A', 'C'], + ['A', 'C'], + ['A', 'C'], + ], }, cols={'s': ['sample_1']}, entries={'HL': [[0.0], [0.0], [0.0]]}, - ).key_rows_by('locus') + ).key_rows_by('locus', 'alleles') self.assertRaisesRegex( SeqrValidationError, - 'Variants are present multiple times in the callset', + "Variants are present multiple times in the callset: \\['1-2-A-C'\\]", validate_no_duplicate_variants, mt, + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, ) def test_validate_expected_contig_frequency(self) -> None: diff --git a/v03_pipeline/lib/misc/vets_test.py b/v03_pipeline/lib/misc/vets_test.py index a22055047..12c4e4467 100644 --- a/v03_pipeline/lib/misc/vets_test.py +++ b/v03_pipeline/lib/misc/vets_test.py @@ -89,7 +89,7 @@ def test_annotate_vets(self) -> None: cols={'s': ['sample_1']}, entries={'HL': [[0.0], [0.0], [0.0], [0.0], [0.0], [0.0]]}, ).key_rows_by('locus', 'alleles') - dragen_mt = split_multi_hts(dragen_mt) + dragen_mt = split_multi_hts(dragen_mt, False) dragen_mt = annotate_vets(dragen_mt) self.assertListEqual( dragen_mt.filters.collect(), diff --git a/v03_pipeline/lib/model/dataset_type.py b/v03_pipeline/lib/model/dataset_type.py index 6e175d42f..daa31ab1b 100644 --- a/v03_pipeline/lib/model/dataset_type.py +++ b/v03_pipeline/lib/model/dataset_type.py @@ -29,6 +29,16 @@ def table_key_type( DatasetType.SV: hl.tstruct(variant_id=hl.tstr), }.get(self, default_key) + def table_key_format_fn( + self, + reference_genome: ReferenceGenome, + ) -> Callable[[hl.StructExpression], str]: + if self in {DatasetType.GCNV, DatasetType.SV}: + return lambda s: s.variant_id + return ( + lambda s: f'{s.locus.contig if reference_genome == ReferenceGenome.GRCh37 else s.locus.contig.replace("chr", "")}-{s.locus.position}-{s.alleles[0]}-{s.alleles[1]}' + ) + @property def col_fields( self, diff --git a/v03_pipeline/lib/paths.py b/v03_pipeline/lib/paths.py index 0e573f62c..2c6b954bb 100644 --- a/v03_pipeline/lib/paths.py +++ b/v03_pipeline/lib/paths.py @@ -109,6 +109,21 @@ def imported_callset_path( ) +def validation_errors_for_run_path( + reference_genome: ReferenceGenome, + dataset_type: DatasetType, + run_id: str, +) -> str: + return os.path.join( + runs_path( + reference_genome, + dataset_type, + ), + run_id, + 'validation_errors.json', + ) + + def metadata_for_run_path( reference_genome: ReferenceGenome, dataset_type: DatasetType, diff --git a/v03_pipeline/lib/paths_test.py b/v03_pipeline/lib/paths_test.py index ad8a659f2..90505fee5 100644 --- a/v03_pipeline/lib/paths_test.py +++ b/v03_pipeline/lib/paths_test.py @@ -24,6 +24,7 @@ sex_check_table_path, valid_filters_path, valid_reference_dataset_collection_path, + validation_errors_for_run_path, variant_annotations_table_path, ) @@ -141,6 +142,16 @@ def test_relatedness_check_table_path(self) -> None: '/seqr/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/relatedness_check/ead56bb177a5de24178e1e622ce1d8beb3f8892bdae1c925d22ca0af4013d6dd.ht', ) + def test_validation_errors_for_run_path(self) -> None: + self.assertEqual( + validation_errors_for_run_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + 'manual__2023-06-26T18:30:09.349671+00:00', + ), + '/seqr/seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/validation_errors.json', + ) + def test_metadata_for_run_path(self) -> None: self.assertEqual( metadata_for_run_path( diff --git a/v03_pipeline/lib/tasks/__init__.py b/v03_pipeline/lib/tasks/__init__.py index b1af69330..7d034326e 100644 --- a/v03_pipeline/lib/tasks/__init__.py +++ b/v03_pipeline/lib/tasks/__init__.py @@ -8,9 +8,6 @@ from v03_pipeline.lib.tasks.migrate_all_variant_annotations_tables import ( MigrateAllVariantAnnotationsTablesTask, ) -from v03_pipeline.lib.tasks.reference_data.update_cached_reference_dataset_queries import ( - UpdateCachedReferenceDatasetQueries, -) from v03_pipeline.lib.tasks.update_lookup_table import ( UpdateLookupTableTask, ) @@ -53,7 +50,6 @@ 'UpdateVariantAnnotationsTableWithNewSamplesTask', 'UpdateVariantAnnotationsTableWithDeletedProjectTask', 'UpdateVariantAnnotationsTableWithDeletedFamiliesTask', - 'UpdateCachedReferenceDatasetQueries', 'WriteMetadataForRunTask', 'WriteProjectFamilyTablesTask', ] diff --git a/v03_pipeline/lib/tasks/base/base_update_variant_annotations_table.py b/v03_pipeline/lib/tasks/base/base_update_variant_annotations_table.py index 14e98fdf4..21b0253b3 100644 --- a/v03_pipeline/lib/tasks/base/base_update_variant_annotations_table.py +++ b/v03_pipeline/lib/tasks/base/base_update_variant_annotations_table.py @@ -13,6 +13,9 @@ ) from v03_pipeline.lib.tasks.base.base_update import BaseUpdateTask from v03_pipeline.lib.tasks.files import GCSorLocalTarget +from v03_pipeline.lib.tasks.reference_data.update_cached_reference_dataset_queries import ( + UpdateCachedReferenceDatasetQueries, +) from v03_pipeline.lib.tasks.reference_data.updated_reference_dataset_collection import ( UpdatedReferenceDatasetCollectionTask, ) @@ -32,19 +35,24 @@ def output(self) -> luigi.Target: ) def requires(self) -> list[luigi.Task]: - return [ - ( - UpdatedReferenceDatasetCollectionTask( - self.reference_genome, - self.dataset_type, - rdc, - ) + requirements = [ + UpdateCachedReferenceDatasetQueries( + reference_genome=self.reference_genome, + dataset_type=self.dataset_type, + ), + ] + requirements.extend( + UpdatedReferenceDatasetCollectionTask( + self.reference_genome, + self.dataset_type, + rdc, ) for rdc in ReferenceDatasetCollection.for_reference_genome_dataset_type( self.reference_genome, self.dataset_type, ) - ] + ) + return requirements def initialize_table(self) -> hl.Table: key_type = self.dataset_type.table_key_type(self.reference_genome) diff --git a/v03_pipeline/lib/tasks/base/base_update_variant_annotations_table_test.py b/v03_pipeline/lib/tasks/base/base_update_variant_annotations_table_test.py index 05f90e097..ce7747768 100644 --- a/v03_pipeline/lib/tasks/base/base_update_variant_annotations_table_test.py +++ b/v03_pipeline/lib/tasks/base/base_update_variant_annotations_table_test.py @@ -53,8 +53,16 @@ def setUp(self) -> None: @patch( 'v03_pipeline.lib.tasks.base.base_update_variant_annotations_table.UpdatedReferenceDatasetCollectionTask', ) - def test_should_create_initialized_table(self, mock_update_rdc_task) -> None: + @patch( + 'v03_pipeline.lib.tasks.base.base_update_variant_annotations_table.UpdateCachedReferenceDatasetQueries', + ) + def test_should_create_initialized_table( + self, + mock_update_crdqs_task, + mock_update_rdc_task, + ) -> None: mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() vat_task = BaseUpdateVariantAnnotationsTableTask( reference_genome=ReferenceGenome.GRCh38, dataset_type=DatasetType.SNV_INDEL, diff --git a/v03_pipeline/lib/tasks/reference_data/update_variant_annotations_table_with_updated_reference_dataset_test.py b/v03_pipeline/lib/tasks/reference_data/update_variant_annotations_table_with_updated_reference_dataset_test.py index 147dfe9e0..b5a5ced2f 100644 --- a/v03_pipeline/lib/tasks/reference_data/update_variant_annotations_table_with_updated_reference_dataset_test.py +++ b/v03_pipeline/lib/tasks/reference_data/update_variant_annotations_table_with_updated_reference_dataset_test.py @@ -649,6 +649,9 @@ @mock.patch( 'v03_pipeline.lib.tasks.base.base_update_variant_annotations_table.UpdatedReferenceDatasetCollectionTask', ) +@mock.patch( + 'v03_pipeline.lib.tasks.base.base_update_variant_annotations_table.UpdateCachedReferenceDatasetQueries', +) @mock.patch( 'v03_pipeline.lib.tasks.base.base_update_variant_annotations_table.BaseUpdateVariantAnnotationsTableTask.initialize_table', ) @@ -719,9 +722,11 @@ def setUp(self) -> None: def test_update_vat_with_updated_rdc_snv_indel_38( self, mock_initialize_table, + mock_update_crdqs_task, mock_update_rdc_task, ): mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() mock_initialize_table.return_value = hl.Table.parallelize( [ hl.Struct( @@ -927,9 +932,11 @@ def test_update_vat_with_updated_rdc_snv_indel_38( def test_update_vat_with_updated_rdc_mito_38( self, mock_initialize_table, + mock_update_crdqs_task, mock_update_rdc_task, ): mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() mock_initialize_table.return_value = hl.Table.parallelize( [ hl.Struct( @@ -1075,9 +1082,11 @@ def test_update_vat_with_updated_rdc_mito_38( def test_update_vat_with_updated_rdc_snv_indel_37( self, mock_initialize_table, + mock_update_crdqs_task, mock_update_rdc_task, ): mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() mock_initialize_table.return_value = hl.Table.parallelize( [ hl.Struct( diff --git a/v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py b/v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py index 9a678786b..5f5445657 100644 --- a/v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py +++ b/v03_pipeline/lib/tasks/update_variant_annotations_table_with_new_samples_test.py @@ -88,6 +88,9 @@ @patch( 'v03_pipeline.lib.tasks.base.base_update_variant_annotations_table.UpdatedReferenceDatasetCollectionTask', ) +@patch( + 'v03_pipeline.lib.tasks.base.base_update_variant_annotations_table.UpdateCachedReferenceDatasetQueries', +) class UpdateVariantAnnotationsTableWithNewSamplesTaskTest(MockedDatarootTestCase): def setUp(self) -> None: super().setUp() @@ -154,9 +157,11 @@ def setUp(self) -> None: def test_missing_pedigree( self, mock_update_vat_with_rdc_task, + mock_update_crdqs_task, mock_update_rdc_task, ) -> None: mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() mock_update_vat_with_rdc_task.return_value = MockCompleteTask() uvatwns_task = UpdateVariantAnnotationsTableWithNewSamplesTask( reference_genome=ReferenceGenome.GRCh38, @@ -180,9 +185,11 @@ def test_missing_pedigree( def test_missing_interval_reference( self, mock_update_vat_with_rdc_task, + mock_update_crdqs_task, mock_update_rdc_task, ) -> None: mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() mock_update_vat_with_rdc_task.return_value = MockCompleteTask() shutil.rmtree( valid_reference_dataset_collection_path( @@ -233,10 +240,12 @@ def test_multiple_update_vat( mock_updated_cached_reference_dataset_query, mock_env: Mock, mock_register_alleles: Mock, + mock_update_crdqs_task, mock_update_rdc_task: Mock, ) -> None: mock_updated_cached_reference_dataset_query.return_value = MockCompleteTask() mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() mock_update_vat_with_rdc_task.return_value = ( BaseUpdateVariantAnnotationsTableTask( reference_genome=ReferenceGenome.GRCh38, @@ -679,9 +688,11 @@ def test_update_vat_grch37( mock_vep: Mock, mock_update_vat_with_rdc_task: Mock, mock_register_alleles: Mock, + mock_update_crdqs_task, mock_update_rdc_task: Mock, ) -> None: mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() mock_update_vat_with_rdc_task.return_value = ( BaseUpdateVariantAnnotationsTableTask( reference_genome=ReferenceGenome.GRCh37, @@ -845,12 +856,14 @@ def test_update_vat_without_accessing_private_datasets( mock_rdc_env: Mock, mock_update_vat_with_rdc_task: Mock, mock_register_alleles: Mock, + mock_update_crdqs_task, mock_update_rdc_task: Mock, ) -> None: mock_load_gencode_ensembl_to_refseq_id.return_value = hl.dict( {'ENST00000327044': 'NM_015658.4'}, ) mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() mock_update_vat_with_rdc_task.return_value = ( BaseUpdateVariantAnnotationsTableTask( reference_genome=ReferenceGenome.GRCh38, @@ -913,9 +926,11 @@ def test_mito_update_vat( self, mock_update_vat_with_rdc_task: Mock, mock_register_alleles: Mock, + mock_update_crdqs_task, mock_update_rdc_task: Mock, ) -> None: mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() mock_update_vat_with_rdc_task.return_value = ( BaseUpdateVariantAnnotationsTableTask( reference_genome=ReferenceGenome.GRCh38, @@ -1198,9 +1213,11 @@ def test_mito_update_vat( def test_sv_update_vat( self, mock_load_gencode: Mock, + mock_update_crdqs_task, mock_update_rdc_task: Mock, ) -> None: mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() mock_load_gencode.return_value = GENE_ID_MAPPING worker = luigi.worker.Worker() update_variant_annotations_task = ( @@ -1778,9 +1795,11 @@ def test_sv_update_vat( def test_gcnv_update_vat( self, + mock_update_crdqs_task, mock_update_rdc_task, ) -> None: mock_update_rdc_task.return_value = MockCompleteTask() + mock_update_crdqs_task.return_value = MockCompleteTask() worker = luigi.worker.Worker() update_variant_annotations_task = ( UpdateVariantAnnotationsTableWithNewSamplesTask( diff --git a/v03_pipeline/lib/tasks/validate_callset.py b/v03_pipeline/lib/tasks/validate_callset.py index c37fe1f37..3b2077446 100644 --- a/v03_pipeline/lib/tasks/validate_callset.py +++ b/v03_pipeline/lib/tasks/validate_callset.py @@ -3,6 +3,7 @@ import luigi.util from v03_pipeline.lib.misc.validation import ( + SeqrValidationError, get_validation_dependencies, validate_allele_type, validate_expected_contig_frequency, @@ -23,6 +24,9 @@ ) from v03_pipeline.lib.tasks.write_imported_callset import WriteImportedCallsetTask from v03_pipeline.lib.tasks.write_sex_check_table import WriteSexCheckTableTask +from v03_pipeline.lib.tasks.write_validation_errors_for_run import ( + WriteValidationErrorsForRunTask, +) @luigi.util.inherits(BaseLoadingRunParams) @@ -88,35 +92,38 @@ def update_table(self, mt: hl.MatrixTable) -> hl.MatrixTable: mt.locus.contig, ), ) - - if not self.skip_validation and self.dataset_type.can_run_validation: - validation_dependencies = get_validation_dependencies( - **self.param_kwargs, - ) - validate_allele_type( - mt, - **self.param_kwargs, - **validation_dependencies, + validation_exceptions = [] + if self.skip_validation or not self.dataset_type.can_run_validation: + return mt.select_globals( + callset_path=self.callset_path, + validated_sample_type=self.sample_type.value, ) - validate_no_duplicate_variants( - mt, - **self.param_kwargs, - **validation_dependencies, - ) - validate_expected_contig_frequency( - mt, - **self.param_kwargs, - **validation_dependencies, - ) - validate_sample_type( - mt, - **self.param_kwargs, - **validation_dependencies, + validation_dependencies = get_validation_dependencies( + **self.param_kwargs, + ) + for validation_f in [ + validate_allele_type, + validate_imputed_sex_ploidy, + validate_no_duplicate_variants, + validate_expected_contig_frequency, + validate_sample_type, + ]: + try: + validation_f( + mt, + **self.param_kwargs, + **validation_dependencies, + ) + except SeqrValidationError as e: # noqa: PERF203 + validation_exceptions.append(e) + if validation_exceptions: + write_validation_errors_for_run_task = self.clone( + WriteValidationErrorsForRunTask, + error_messages=[str(e) for e in validation_exceptions], ) - validate_imputed_sex_ploidy( - mt, - **self.param_kwargs, - **validation_dependencies, + write_validation_errors_for_run_task.run() + raise SeqrValidationError( + write_validation_errors_for_run_task.to_single_error_message(), ) return mt.select_globals( callset_path=self.callset_path, diff --git a/v03_pipeline/lib/tasks/validate_callset_test.py b/v03_pipeline/lib/tasks/validate_callset_test.py new file mode 100644 index 000000000..178b71284 --- /dev/null +++ b/v03_pipeline/lib/tasks/validate_callset_test.py @@ -0,0 +1,92 @@ +import json +import shutil +from unittest.mock import Mock, patch + +import luigi.worker + +from v03_pipeline.lib.model import ( + CachedReferenceDatasetQuery, + DatasetType, + ReferenceGenome, + SampleType, +) +from v03_pipeline.lib.paths import ( + cached_reference_dataset_query_path, +) +from v03_pipeline.lib.tasks.validate_callset import ( + ValidateCallsetTask, +) +from v03_pipeline.lib.tasks.write_validation_errors_for_run import ( + WriteValidationErrorsForRunTask, +) +from v03_pipeline.lib.test.mock_complete_task import MockCompleteTask +from v03_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase + +TEST_CODING_NONCODING_CRDQ_1 = ( + 'v03_pipeline/var/test/reference_data/test_gnomad_coding_noncoding_crdq_1.ht' +) +MULTIPLE_VALIDATION_EXCEPTIONS_VCF = ( + 'v03_pipeline/var/test/callsets/multiple_validation_exceptions.vcf' +) + +TEST_RUN_ID = 'manual__2024-04-03' + + +class ValidateCallsetTest(MockedDatarootTestCase): + def setUp(self) -> None: + super().setUp() + shutil.copytree( + TEST_CODING_NONCODING_CRDQ_1, + cached_reference_dataset_query_path( + ReferenceGenome.GRCh38, + DatasetType.SNV_INDEL, + CachedReferenceDatasetQuery.GNOMAD_CODING_AND_NONCODING_VARIANTS, + ), + ) + + @patch( + 'v03_pipeline.lib.tasks.validate_callset.UpdatedCachedReferenceDatasetQuery', + ) + def test_validate_callset_multiple_exceptions( + self, + mock_updated_cached_reference_dataset_query: Mock, + ) -> None: + mock_updated_cached_reference_dataset_query.return_value = MockCompleteTask() + worker = luigi.worker.Worker() + validate_callset_task = ValidateCallsetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + # NB: + # This callset contains duplicate rows for chr1:902088, + # a NON_REF allele type at position chr1: 902024, missing + # all contigs but chr1, and contains non-coding variants. + callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, + skip_validation=False, + run_id=TEST_RUN_ID, + ) + worker.add(validate_callset_task) + worker.run() + self.assertFalse(validate_callset_task.complete()) + + write_validation_errors_task = WriteValidationErrorsForRunTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.SNV_INDEL, + sample_type=SampleType.WES, + callset_path=MULTIPLE_VALIDATION_EXCEPTIONS_VCF, + skip_validation=False, + run_id=TEST_RUN_ID, + ) + self.assertTrue(write_validation_errors_task.complete()) + with write_validation_errors_task.output().open('r') as f: + self.assertDictEqual( + json.load(f), + { + 'error_messages': [ + "Alleles with invalid AlleleType are present in the callset: [('G', '')]", + "Variants are present multiple times in the callset: ['1-902088-G-A']", + 'Missing the following expected contigs:chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX', + 'Sample type validation error: dataset sample-type is specified as WES but appears to be WGS because it contains many common non-coding variants', + ], + }, + ) diff --git a/v03_pipeline/lib/tasks/write_imported_callset.py b/v03_pipeline/lib/tasks/write_imported_callset.py index 6235988f6..90bba9ebf 100644 --- a/v03_pipeline/lib/tasks/write_imported_callset.py +++ b/v03_pipeline/lib/tasks/write_imported_callset.py @@ -10,6 +10,7 @@ split_multi_hts, ) from v03_pipeline.lib.misc.validation import ( + SeqrValidationError, validate_imported_field_types, ) from v03_pipeline.lib.misc.vets import annotate_vets @@ -21,6 +22,9 @@ from v03_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams from v03_pipeline.lib.tasks.base.base_write import BaseWriteTask from v03_pipeline.lib.tasks.files import CallsetTask, GCSorLocalTarget +from v03_pipeline.lib.tasks.write_validation_errors_for_run import ( + WriteValidationErrorsForRunTask, +) @luigi.util.inherits(BaseLoadingRunParams) @@ -62,50 +66,64 @@ def requires(self) -> list[luigi.Task]: ] def create_table(self) -> hl.MatrixTable: - mt = import_callset( - self.callset_path, - self.reference_genome, - self.dataset_type, - ) - filters_path = None - if ( - Env.EXPECT_WES_FILTERS - and not self.skip_expect_filters - and self.dataset_type.expect_filters( - self.sample_type, + try: + # NB: throws SeqrValidationError + mt = import_callset( + self.callset_path, + self.reference_genome, + self.dataset_type, ) - ): - filters_path = valid_filters_path( + filters_path = None + if ( + Env.EXPECT_WES_FILTERS + and not self.skip_expect_filters + and self.dataset_type.expect_filters( + self.sample_type, + ) + ): + filters_path = valid_filters_path( + self.dataset_type, + self.sample_type, + self.callset_path, + ) + filters_ht = import_vcf(filters_path, self.reference_genome).rows() + mt = mt.annotate_rows(filters=filters_ht[mt.row_key].filters) + additional_row_fields = get_additional_row_fields( + mt, self.dataset_type, - self.sample_type, - self.callset_path, + self.skip_check_sex_and_relatedness, ) - filters_ht = import_vcf(filters_path, self.reference_genome).rows() - mt = mt.annotate_rows(filters=filters_ht[mt.row_key].filters) - additional_row_fields = get_additional_row_fields( - mt, - self.dataset_type, - self.skip_check_sex_and_relatedness, - ) - mt = select_relevant_fields( - mt, - self.dataset_type, - additional_row_fields, - ) - # This validation isn't override-able by the skip option. - # If a field is the wrong type, the pipeline will likely hard-fail downstream. - validate_imported_field_types( - mt, - self.dataset_type, - additional_row_fields, - ) - if self.dataset_type.has_multi_allelic_variants: - mt = split_multi_hts(mt) - # Special handling of variant-level filter annotation for VETs filters. - # The annotations are present on the sample-level FT field but are - # expected upstream on "filters". - mt = annotate_vets(mt) - return mt.select_globals( - callset_path=self.callset_path, - filters_path=filters_path or hl.missing(hl.tstr), - ) + # NB: throws SeqrValidationError + mt = select_relevant_fields( + mt, + self.dataset_type, + additional_row_fields, + ) + # This validation isn't override-able by the skip option. + # If a field is the wrong type, the pipeline will likely hard-fail downstream. + # NB: throws SeqrValidationError + validate_imported_field_types( + mt, + self.dataset_type, + additional_row_fields, + ) + if self.dataset_type.has_multi_allelic_variants: + # NB: throws SeqrValidationError + mt = split_multi_hts(mt, self.skip_validation) + # Special handling of variant-level filter annotation for VETs filters. + # The annotations are present on the sample-level FT field but are + # expected upstream on "filters". + mt = annotate_vets(mt) + return mt.select_globals( + callset_path=self.callset_path, + filters_path=filters_path or hl.missing(hl.tstr), + ) + except SeqrValidationError as e: + write_validation_errors_for_run_task = self.clone( + WriteValidationErrorsForRunTask, + error_messages=[str(e)], + ) + write_validation_errors_for_run_task.run() + raise SeqrValidationError( + write_validation_errors_for_run_task.to_single_error_message(), + ) from e diff --git a/v03_pipeline/lib/tasks/write_metadata_for_run.py b/v03_pipeline/lib/tasks/write_metadata_for_run.py index 4e9d2fdea..e04acbbad 100644 --- a/v03_pipeline/lib/tasks/write_metadata_for_run.py +++ b/v03_pipeline/lib/tasks/write_metadata_for_run.py @@ -27,9 +27,6 @@ def output(self) -> luigi.Target: ), ) - def complete(self) -> bool: - return GCSorLocalTarget(self.output().path).exists() - def requires(self) -> list[luigi.Task]: return [ self.clone( diff --git a/v03_pipeline/lib/tasks/write_relatedness_check_table.py b/v03_pipeline/lib/tasks/write_relatedness_check_table.py index 3e1b22288..edfe0d716 100644 --- a/v03_pipeline/lib/tasks/write_relatedness_check_table.py +++ b/v03_pipeline/lib/tasks/write_relatedness_check_table.py @@ -3,7 +3,7 @@ import luigi.util from v03_pipeline.lib.methods.relatedness import call_relatedness -from v03_pipeline.lib.model import CachedReferenceDatasetQuery, Env +from v03_pipeline.lib.model import CachedReferenceDatasetQuery from v03_pipeline.lib.paths import ( relatedness_check_table_path, ) @@ -27,21 +27,14 @@ def output(self) -> luigi.Target: ), ) - def requires(self) -> luigi.Task: - requirements = [ + def requires(self): + return [ self.clone(ValidateCallsetTask), + self.clone( + UpdatedCachedReferenceDatasetQuery, + crdq=CachedReferenceDatasetQuery.GNOMAD_QC, + ), ] - if Env.ACCESS_PRIVATE_REFERENCE_DATASETS: - requirements = [ - *requirements, - ( - self.clone( - UpdatedCachedReferenceDatasetQuery, - crdq=CachedReferenceDatasetQuery.GNOMAD_QC, - ) - ), - ] - return requirements def create_table(self) -> hl.Table: callset_mt = hl.read_matrix_table(self.input()[0].path) diff --git a/v03_pipeline/lib/tasks/write_validation_errors_for_run.py b/v03_pipeline/lib/tasks/write_validation_errors_for_run.py new file mode 100644 index 000000000..eaefb0e8c --- /dev/null +++ b/v03_pipeline/lib/tasks/write_validation_errors_for_run.py @@ -0,0 +1,36 @@ +import json + +import luigi +import luigi.util + +from v03_pipeline.lib.paths import validation_errors_for_run_path +from v03_pipeline.lib.tasks.base.base_loading_run_params import BaseLoadingRunParams +from v03_pipeline.lib.tasks.files import GCSorLocalTarget + + +@luigi.util.inherits(BaseLoadingRunParams) +class WriteValidationErrorsForRunTask(luigi.Task): + error_messages = luigi.ListParameter(default=[]) + + def to_single_error_message(self) -> str: + with self.output().open('r') as f: + error_messages = json.load(f)['error_messages'] + if len(error_messages) == 1: + return error_messages[0] + return f'Multiple validation errors encountered: {error_messages}' + + def output(self) -> luigi.Target: + return GCSorLocalTarget( + validation_errors_for_run_path( + self.reference_genome, + self.dataset_type, + self.run_id, + ), + ) + + def run(self) -> None: + validation_errors_json = { + 'error_messages': self.error_messages, + } + with self.output().open('w') as f: + json.dump(validation_errors_json, f) diff --git a/v03_pipeline/lib/tasks/write_variant_annotations_vcf_test.py b/v03_pipeline/lib/tasks/write_variant_annotations_vcf_test.py index ea1ef11f8..4a6b4baec 100644 --- a/v03_pipeline/lib/tasks/write_variant_annotations_vcf_test.py +++ b/v03_pipeline/lib/tasks/write_variant_annotations_vcf_test.py @@ -10,6 +10,7 @@ from v03_pipeline.lib.tasks.write_variant_annotations_vcf import ( WriteVariantAnnotationsVCF, ) +from v03_pipeline.lib.test.mock_complete_task import MockCompleteTask from v03_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase TEST_SV_VCF = 'v03_pipeline/var/test/callsets/sv_1.vcf' @@ -39,11 +40,16 @@ class WriteVariantAnnotationsVCFTest(MockedDatarootTestCase): @patch( 'v03_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', ) + @patch( + 'v03_pipeline.lib.tasks.base.base_update_variant_annotations_table.UpdateCachedReferenceDatasetQueries', + ) def test_sv_export_vcf( self, + mock_update_crdqs_task: Mock, mock_load_gencode: Mock, ) -> None: mock_load_gencode.return_value = GENE_ID_MAPPING + mock_update_crdqs_task.return_value = MockCompleteTask() worker = luigi.worker.Worker() update_variant_annotations_task = ( UpdateVariantAnnotationsTableWithNewSamplesTask( diff --git a/v03_pipeline/var/test/callsets/multiple_validation_exceptions.vcf b/v03_pipeline/var/test/callsets/multiple_validation_exceptions.vcf new file mode 100644 index 000000000..2878c1f6b --- /dev/null +++ b/v03_pipeline/var/test/callsets/multiple_validation_exceptions.vcf @@ -0,0 +1,159 @@ +##fileformat=VCFv4.2 +##hailversion=0.2.8-70304a52d33d +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= 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AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-7.95400e+00;DB;DP=484;Dels=0.00000e+00;FS=7.13100e+00;HaplotypeScore=3.21100e-01;InbreedingCoeff=-6.80000e-03;MQ=5.85800e+01;MQ0=1;MQRankSum=7.38500e+00;QD=1.23600e+01;ReadPosRankSum=-7.54000e-01;SNPEFF_AMINO_ACID_CHANGE=S200;SNPEFF_CODON_CHANGE=agC/agT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_874655_874840;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=5.39000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs145967298|1|63|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|683|600|200|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||7/14|||ENST00000342066.3:c.600N>T|ENST00000342066.3:c.600N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.293255131964809||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs145967298|1|4850|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|upstream_gene_variant||||||rs145967298|1|2812|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|upstream_gene_variant||||||rs145967298|1|2749|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|upstream_gene_variant||||||rs145967298|1|1722|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs145967298|1|4850|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|synonymous_variant|80|81|27|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||1/7|||ENST00000455979.1:c.80N>T|ENST00000455979.1:c.80N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.0498461538461538||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000187634|ENST00000437963|Transcript|downstream_gene_variant||||||rs145967298|1|3561|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000393181||Q5SV95_HUMAN&I7FV93_HUMAN|UPI000155D47B||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000478729|Transcript|upstream_gene_variant||||||rs145967298|1|992|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs145967298|1|4851|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|371|372|124|S|agC/agT|rs145967298|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||5/12|||ENST00000341065.4:c.371N>T|ENST00000341065.4:c.371N>T(p.%3D)|T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||POSITION:0.210288298473714||NON_CAN_SPLICE_SURR|||||||,T||ENSR00001516735|RegulatoryFeature|regulatory_region_variant||||||rs145967298|1||||||regulatory_region|||||||||||||||T:0.0009||T:0.01|||T:0.000227|T:0.001628||||||||||||||||| GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,111,1368 0/0:24,0:24:66:0,66,870 0/0:32,0:32:96:0,96,1183 0/0:8,0:8:24:0,24,245 0/0:8,0:8:24:0,24,267 0/0:9,0:9:27:0,27,318 0/0:26,0:26:75:0,75,879 0/0:31,0:31:93:0,93,1120 0/0:39,0:39:99:0,117,1375 0/0:56,0:56:99:0,169,2023 0/1:21,22:42:99:519,0,613 0/0:29,0:29:87:0,87,1048 0/0:43,0:43:99:0,129,1556 0/0:20,0:20:60:0,60,741 0/0:45,0:45:99:0,135,1586 0/0:35,0:35:99:0,105,1239 +1 876499 rs4372192 A G 212847.01 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=2.42570e+01;DB;DP=122;Dels=1.00000e-02;FS=9.96800e+00;HaplotypeScore=2.51500e-01;InbreedingCoeff=4.11000e-02;MQ=5.91300e+01;MQ0=0;MQRankSum=7.64000e-01;QD=3.03200e+01;ReadPosRankSum=2.13900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.70000e+00;culprit=MQ;CSQ=G|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs4372192|1|1828|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs4372192|1|4200|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000342066|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||7/13||ENST00000342066.3:c.707-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1683||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs4372192|1|3085|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000187634|ENST00000464948|Transcript|upstream_gene_variant||||||rs4372192|1|1047|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000466827|Transcript|upstream_gene_variant||||||rs4372192|1|984|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000474461|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|44|||||rs4372192|1||1|SAMD11|HGNC|28706|retained_intron||||||||||1/4|||ENST00000474461.1:n.44N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000455979|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||1/6||ENST00000455979.1:c.187-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1683||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs4372192|1|3085|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000478729|Transcript|intron_variant&non_coding_transcript_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|processed_transcript|||||||||||1/2||ENST00000478729.1:n.118-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs4372192|1|3086|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676|||||||||||||||||,G|ENSG00000187634|ENST00000341065|Transcript|intron_variant||||||rs4372192|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||5/11||ENST00000341065.4:c.430-25N>G||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||INTRON_SIZE:1731||NON_CAN_SPLICE&ANC_ALLELE|||||||,G||ENSR00000528857|RegulatoryFeature|regulatory_region_variant||||||rs4372192|1||||||regulatory_region|||||||||||||||A:0.0822|G:0.86|G:0.92|G:0.92|G:0.95|G:0.883310|G:0.937676||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,7:7:21:253,21,0 1/1:0,8:8:24:296,24,0 1/1:0,4:4:12:148,12,0 1/1:0,5:5:15:184,15,0 1/1:0,1:1:3:39,3,0 1/1:0,5:5:15:176,15,0 1/1:0,9:9:27:316,27,0 1/1:0,11:11:33:397,33,0 1/1:0,7:7:18:212,18,0 1/1:0,11:11:27:369,27,0 1/1:0,13:13:39:492,39,0 0/1:7,9:15:99:235,0,158 1/1:0,7:7:18:231,18,0 1/1:0,4:4:12:154,12,0 1/1:0,8:8:24:296,24,0 1/1:0,7:7:21:270,21,0 +1 878314 rs142558220 G C 2808.55 PASS AC=3;AF=9.40000e-02;AN=32;BaseQRankSum=1.88800e+00;DB;DP=117;Dels=0.00000e+00;FS=1.06220e+01;HaplotypeScore=2.21900e-01;InbreedingCoeff=3.64000e-02;MQ=5.94000e+01;MQ0=1;MQRankSum=1.65200e+00;QD=9.46000e+00;ReadPosRankSum=-3.88300e+00;SNPEFF_AMINO_ACID_CHANGE=G480;SNPEFF_CODON_CHANGE=ggG/ggC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_877939_878438;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=6.85000e+00;culprit=QD;CSQ=C|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|3643|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|2385|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000342066|Transcript|synonymous_variant|1523|1440|480|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||11/14|||ENST00000342066.3:c.1440N>C|ENST00000342066.3:c.1440N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.703812316715543||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1270|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|42|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|132|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000474461|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|802|||||rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|retained_intron||||||||||4/4|||ENST00000474461.1:n.802N>C||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000455979|Transcript|synonymous_variant|920|921|307|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||5/7|||ENST00000455979.1:c.920N>C|ENST00000455979.1:c.920N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.566769230769231||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1270|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|761|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs142558220&COSM426784|1|1271|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1|||||||||||||||,C|ENSG00000187634|ENST00000341065|Transcript|synonymous_variant|1163|1164|388|G|ggG/ggC|rs142558220&COSM426784|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||9/12|||ENST00000341065.4:c.1163N>C|ENST00000341065.4:c.1163N>C(p.%3D)|C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||POSITION:0.65799886941775||NON_CAN_SPLICE_SURR|||||||,C||ENSR00000528857|RegulatoryFeature|regulatory_region_variant||||||rs142558220&COSM426784|1||||||regulatory_region|||||||||||||||C:0.0482|C:0.01|C:0.06||C:0.10|C:0.013449|C:0.066877||0&1||||||||||||||| GT:AD:DP:GQ:PL 0/1:2,1:3:30:30,0,67 0/0:2,0:2:6:0,6,82 0/1:2,3:5:61:93,0,61 0/0:2,0:2:6:0,6,72 0/0:1,0:1:3:0,3,37 0/1:2,3:5:54:93,0,54 0/0:16,0:16:45:0,45,560 0/0:5,0:5:15:0,15,188 0/0:12,0:12:33:0,33,414 0/0:10,0:10:30:0,30,393 0/0:16,0:16:48:0,48,617 0/0:5,0:5:15:0,15,181 0/0:5,0:5:15:0,15,193 0/0:13,0:13:36:0,36,439 0/0:9,0:9:24:0,24,317 0/0:8,0:8:21:0,21,276 +1 878809 rs191952374 C T 1761.84 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-7.95300e+00;DB;DP=453;Dels=0.00000e+00;FS=1.68300e+00;HaplotypeScore=2.28500e-01;InbreedingCoeff=-3.10000e-03;MQ=5.91000e+01;MQ0=0;MQRankSum=1.29700e+00;QD=1.36600e+01;ReadPosRankSum=-8.52000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=9.25000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs191952374|1|4138|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs191952374|1|1890|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||12/13||ENST00000342066.3:c.1689+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs191952374|1|775|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs191952374|1|537|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs191952374|1|627|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs191952374|1|435|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||6/6||ENST00000455979.1:c.1169+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs191952374|1|775|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs191952374|1|1256|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs191952374|1|776|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|intron_variant||||||rs191952374|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||10/11||ENST00000341065.4:c.1412+52N>T||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||INTRON_SIZE:320||NON_CAN_SPLICE|||||||,T||ENSR00000528858|RegulatoryFeature|regulatory_region_variant||||||rs191952374|1||||||regulatory_region|||||||||||||||T:0.0046||T:0.01||T:0.01|T:0.000398|T:0.008636||||||||||||||||| GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,105,1323 0/0:24,0:24:72:0,72,960 0/0:31,0:31:93:0,93,1172 0/0:10,0:10:30:0,30,376 0/0:10,0:10:30:0,30,370 0/0:12,0:12:36:0,36,453 0/0:35,0:35:99:0,105,1376 0/0:33,0:33:99:0,99,1273 0/0:31,0:31:93:0,93,1240 0/0:33,0:33:96:0,96,1192 0/0:33,0:33:99:0,99,1281 0/0:25,0:25:75:0,75,983 0/1:18,16:33:99:488,0,504 0/0:33,0:33:99:0,99,1273 0/0:44,0:44:99:0,132,1698 0/0:31,0:31:90:0,90,1198 +1 879576 rs115979567 C T 18648.64 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-2.26830e+01;DB;DP=839;Dels=0.00000e+00;FS=2.49350e+01;HaplotypeScore=4.12600e-01;InbreedingCoeff=-2.18000e-02;MQ=5.92100e+01;MQ0=1;MQRankSum=1.02100e+00;QD=1.36100e+01;ReadPosRankSum=7.91400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.39000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187634|ENST00000420190|Transcript|downstream_gene_variant||||||rs115979567|1|4905|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000411579||Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI000155D47C||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|downstream_gene_variant||||||rs115979567|1|1123|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|3_prime_UTR_variant|2172|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||14/14|||ENST00000342066.3:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000327044|Transcript|downstream_gene_variant||||||rs115979567|1|8|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs115979567|1|1304|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs115979567|1|1394|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs115979567|1|1202|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|3_prime_UTR_variant|1668|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||7/7|||ENST00000455979.1:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000188976|ENST00000483767|Transcript|downstream_gene_variant||||||rs115979567|1|8|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs115979567|1|2023|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000188976|ENST00000477976|Transcript|downstream_gene_variant||||||rs115979567|1|9|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|3_prime_UTR_variant|1812|||||rs115979567|1||1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||12/12|||ENST00000341065.4:c.*43N>T||T:0.0266|T:0.11|T:0.01||T:0.0013|T:0.061404|T:0.000120||||||||||NON_CAN_SPLICE_SURR||||||| GT:AD:DP:GQ:PL 0/0:66,0:66:99:0,199,2441 0/1:25,28:51:99:767,0,834 0/0:55,0:55:99:0,166,2079 0/0:11,0:11:33:0,33,392 0/0:15,0:15:45:0,45,554 0/0:17,0:17:51:0,51,622 0/0:50,0:50:99:0,150,1966 0/0:65,0:65:99:0,196,2507 0/0:60,0:60:99:0,181,2268 0/0:70,0:70:99:0,211,2589 0/0:64,0:64:99:0,193,2452 0/0:65,0:65:99:0,196,2507 0/0:56,0:56:99:0,169,2117 0/0:60,0:60:99:0,181,2359 0/0:79,0:79:99:0,238,2986 0/0:55,0:55:99:0,165,2099 +1 881070 rs41285794 G A 20769.13 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-9.52200e+00;DB;DP=1185;Dels=0.00000e+00;FS=1.15500e+01;HaplotypeScore=1.69500e-01;InbreedingCoeff=-1.83000e-02;MQ=5.90700e+01;MQ0=0;MQRankSum=1.85940e+01;QD=1.31500e+01;ReadPosRankSum=-8.90700e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=4.22000e+00;culprit=InbreedingCoeff;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs41285794|1|128|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs41285794|1|1115|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||16/18||ENST00000327044.6:c.1918-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||INTRON_SIZE:519||NON_CAN_SPLICE|||||||,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs41285794|1|2798|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs41285794|1|2888|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs41285794|1|2696|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs41285794|1|1431|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|intron_variant&non_coding_transcript_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||2/4||ENST00000483767.1:n.774-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs41285794|1|3517|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs41285794|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||14/16||ENST00000477976.1:n.3365-37N>T||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs41285794|1|1115|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0051|A:0.0020|A:0.01||A:0.01|A:0.002497|A:0.009651||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:78,0:78:99:0,235,2947 0/0:66,0:66:99:0,199,2595 0/0:59,0:59:99:0,178,2182 0/0:37,0:37:99:0,111,1365 0/0:36,0:36:99:0,108,1331 0/0:33,0:33:99:0,99,1192 0/0:69,0:69:99:0,208,2662 0/0:88,0:88:99:0,265,3395 0/0:98,0:98:99:0,295,3781 0/1:36,31:64:99:982,0,1021 0/0:86,0:86:99:0,259,3318 0/0:93,0:93:99:0,280,3588 0/0:92,0:92:99:0,277,3549 0/0:102,0:102:99:0,307,3935 0/0:89,0:89:99:0,268,3433 0/0:95,0:95:99:0,286,3665 +1 881627 rs2272757 G A 411792.28 PASS AC=22;AF=6.88000e-01;AN=32;BaseQRankSum=-3.32930e+01;DB;DP=644;Dels=0.00000e+00;FS=2.51600e+00;HaplotypeScore=5.86200e-01;InbreedingCoeff=3.09600e-01;MQ=5.88200e+01;MQ0=7;MQRankSum=6.81600e+00;QD=2.28900e+01;ReadPosRankSum=1.01500e+00;SNPEFF_AMINO_ACID_CHANGE=L615;SNPEFF_CODON_CHANGE=Ctg/Ttg;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_881553_881666;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=4.35000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs2272757&COSM1344685|1|685|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1672|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1893|1843|615|L|Ctg/Ttg|rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||16/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1843N>T|ENST00000327044.6:c.1843N>T(p.%3D)|A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||POSITION:0.819111111111111||NON_CAN_SPLICE_SURR|||||||,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3355|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3445|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|3253|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1988|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|699|||||rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||2/5|||ENST00000483767.1:n.699N>T||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|4074|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3290|||||rs2272757&COSM1344685|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||14/17|||ENST00000477976.1:n.3290N>T||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1|||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs2272757&COSM1344685|1|1672|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.4743|A:0.08|A:0.46|A:0.61|A:0.63|A:0.156222|A:0.637907||0&1||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 1/1:0,39:38:99:1384,111,0 0/0:61,0:61:99:0,184,2353 0/1:24,17:38:99:494,0,613 1/1:0,16:16:48:550,48,0 1/1:0,18:18:54:649,54,0 1/1:0,25:25:66:826,66,0 1/1:0,51:51:99:1886,153,0 0/1:25,23:46:99:661,0,639 1/1:0,33:33:99:1220,99,0 1/1:0,52:52:99:1879,156,0 1/1:0,45:45:99:1701,135,0 0/0:58,0:58:99:0,175,2237 0/1:17,18:34:99:523,0,478 1/1:0,44:44:99:1627,132,0 0/1:20,25:41:99:674,0,488 0/0:44,1:44:99:0,120,1521 +1 881918 rs35471880 G A 26418.87 PASS AC=5;AF=1.56000e-01;AN=32;BaseQRankSum=6.25300e+00;DB;DP=1040;Dels=0.00000e+00;FS=2.27620e+01;HaplotypeScore=2.29500e-01;InbreedingCoeff=-2.81000e-02;MQ=5.57400e+01;MQ0=40;MQRankSum=1.69390e+01;QD=1.18200e+01;ReadPosRankSum=-6.75000e-01;SNPEFF_AMINO_ACID_CHANGE=S556L;SNPEFF_CODON_CHANGE=tCg/tTg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_881782_881925;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=1.82000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs35471880|1|976|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs35471880|1|1963|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|missense_variant|1717|1667|556|S/L|tCg/tTg|rs35471880|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|deleterious(0.03)|benign(0.311)|15/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1667N>T|ENSP00000317992.6:p.Ser556Leu|A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||POSITION:0.740888888888889||NON_CAN_SPLICE_SURR||B%3BB%3BB|16.43|D|T|D|T,A|ENSG00000187634|ENST00000464948|Transcript|downstream_gene_variant||||||rs35471880|1|3646|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000466827|Transcript|downstream_gene_variant||||||rs35471880|1|3736|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000474461|Transcript|downstream_gene_variant||||||rs35471880|1|3544|1|SAMD11|HGNC|28706|retained_intron|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs35471880|1|2279|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000483767|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|523|||||rs35471880|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||1/5|||ENST00000483767.1:n.523N>T||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000478729|Transcript|downstream_gene_variant||||||rs35471880|1|4365|1|SAMD11|HGNC|28706|processed_transcript|||||||||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3114|||||rs35471880|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||13/17|||ENST00000477976.1:n.3114N>T||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs35471880|1|1963|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0257|A:0.01|A:0.03||A:0.06|A:0.014980|A:0.061628||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:73,0:73:99:0,220,2699 0/0:70,0:70:99:0,211,2589 0/0:66,0:66:99:0,199,2385 0/1:12,18:29:99:475,0,278 0/0:28,0:28:78:0,78,843 0/1:18,10:27:99:271,0,511 0/1:34,36:67:99:876,0,921 0/1:37,38:74:99:966,0,944 0/0:69,0:69:99:0,208,2493 0/0:93,0:93:99:0,280,3279 0/1:41,32:70:99:777,0,1118 0/0:76,0:76:99:0,229,2746 0/0:73,0:73:99:0,220,2573 0/0:69,0:69:99:0,208,2493 0/0:82,0:82:99:0,247,2963 0/0:74,0:74:99:0,223,2609 +1 883485 . C T 81.94 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-3.68100e+00;DP=94;Dels=0.00000e+00;FS=0.00000e+00;HaplotypeScore=1.64200e-01;InbreedingCoeff=-2.46000e-02;MQ=5.53400e+01;MQ0=0;MQRankSum=3.55900e+00;QD=3.03000e+00;ReadPosRankSum=-1.07900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-3.92700e-01;culprit=MQ;CSQ=T|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs374301410|1|1045|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs374301410|1|3846|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs374301410|1|2543|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs374301410|1|3530|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs374301410|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||14/18||ENST00000327044.6:c.1659+26N>A|||||||T:0|T:0.000117||||||||INTRON_SIZE:1585||NON_CAN_SPLICE|||||||,T|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs374301410|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||12/16||ENST00000477976.1:n.3106+26N>A|||||||T:0|T:0.000117|||||||||||||||||,T|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs374301410|1|3530|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A|||||||||||||T:0|T:0.000117||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:8,0:8:24:0,24,304 0/0:3,0:3:9:0,9,118 0/0:5,0:5:15:0,15,178 0/0:5,0:5:15:0,15,181 0/0:2,0:2:6:0,6,69 0/0:4,0:5:12:0,12,145 0/0:6,0:6:18:0,18,217 0/0:10,0:10:30:0,30,378 0/0:11,0:11:33:0,33,411 0/1:5,1:6:14:14,0,181 0/0:10,0:10:30:0,30,373 0/0:4,0:4:9:0,9,114 0/0:5,0:5:15:0,15,193 0/0:4,0:4:12:0,12,157 0/0:6,0:6:18:0,18,229 0/0:3,0:4:9:0,9,122 +1 883625 rs4970378 A G 232503.78 PASS AC=30;AF=1.00000e+00;AN=30;DB;DP=117;Dels=0.00000e+00;FS=0.00000e+00;HaplotypeScore=1.37000e-01;InbreedingCoeff=-1.43000e-02;MQ=5.74300e+01;MQ0=0;QD=3.66300e+01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VQSLOD=-2.60400e-01;culprit=MQ;CSQ=G|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs4970378|1|1185|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs4970378|1|3986|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs4970378|1|2683|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs4970378|1|3670|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs4970378|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||13/18||ENST00000327044.6:c.1558-13N>C||A:0.0000|||||G:0.999543|||||||||INTRON_SIZE:257||NON_CAN_SPLICE&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs4970378|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||11/16||ENST00000477976.1:n.3005-13N>C||A:0.0000|||||G:0.999543||||||||||||||||||,G|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs4970378|1|3670|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0000|||||G:0.999543|||||||||||EXON_INTRON_UNDEF&ANC_ALLELE||||||| GT:AD:DP:GQ:PL 1/1:0,4:4:12:151,12,0 1/1:0,3:3:9:118,9,0 1/1:0,6:6:18:212,18,0 1/1:0,5:5:15:185,15,0 ./.:.:.:.:. 1/1:0,4:4:12:142,12,0 1/1:0,13:13:39:501,39,0 1/1:0,8:8:21:276,21,0 1/1:0,19:19:57:718,57,0 1/1:0,9:9:27:340,27,0 1/1:0,12:12:36:454,36,0 1/1:0,4:4:12:151,12,0 1/1:0,5:5:15:198,15,0 1/1:0,16:16:48:605,48,0 1/1:0,3:3:9:119,9,0 1/1:0,5:6:15:191,15,0 +1 883918 rs139116730 G A 4594.12 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=6.89000e+00;DB;DP=1146;Dels=0.00000e+00;FS=4.31330e+01;HaplotypeScore=8.65000e-02;InbreedingCoeff=-4.00000e-03;MQ=5.62500e+01;MQ0=14;MQRankSum=1.10440e+01;QD=1.07800e+01;ReadPosRankSum=-1.97100e+00;SNPEFF_AMINO_ACID_CHANGE=S503;SNPEFF_CODON_CHANGE=tcC/tcT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_883870_883983;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=5.95000e-01;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000483767|Transcript|upstream_gene_variant||||||rs139116730|1|1478|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000455979|Transcript|downstream_gene_variant||||||rs139116730|1|4279|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000412228|||UPI000155D479||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000496938|Transcript|upstream_gene_variant||||||rs139116730|1|2976|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000342066|Transcript|downstream_gene_variant||||||rs139116730|1|3963|1|SAMD11|HGNC|28706|protein_coding|YES||CCDS2.2|ENSP00000342313|SAM11_HUMAN|Q5SV95_HUMAN&I7FV93_HUMAN&A6PWC8_HUMAN|UPI0000D61E04||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1559|1509|503|S|tcC/tcT|rs139116730|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||13/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1509N>T|ENST00000327044.6:c.1509N>T(p.%3D)|A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||POSITION:0.670666666666667||NON_CAN_SPLICE_SURR|||||||,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2956|||||rs139116730|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||11/17|||ENST00000477976.1:n.2956N>T||A:0.0005||||A:0.0013|A:0.000227|A:0.003488|||||||||||||||||,A|ENSG00000187634|ENST00000341065|Transcript|downstream_gene_variant||||||rs139116730|1|3963|1|SAMD11|HGNC|28706|protein_coding||||ENSP00000349216|||UPI000155D47A||||||||A:0.0005||||A:0.0013|A:0.000227|A:0.003488||||||||||EXON_INTRON_UNDEF||||||| GT:AD:DP:GQ:PL 0/0:76,0:76:99:0,229,2746 0/0:47,0:47:99:0,141,1738 0/0:75,0:75:99:0,226,2710 0/0:36,0:36:99:0,108,1201 0/0:37,0:37:99:0,111,1271 0/0:42,0:42:99:0,126,1443 0/0:74,0:74:99:0,223,2609 0/0:82,0:82:99:0,247,2963 0/0:120,0:120:99:0,361,4336 0/0:96,0:96:99:0,289,3468 0/1:38,33:68:99:823,0,921 0/0:78,0:78:99:0,235,2818 0/0:56,0:56:99:0,169,1974 0/0:92,0:92:99:0,277,3402 0/0:78,0:78:99:0,235,2884 0/0:89,0:89:99:0,268,3216 +1 887560 rs3748595 A C 806833.88 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=5.43470e+01;DB;DP=472;Dels=0.00000e+00;FS=1.69080e+01;HaplotypeScore=2.91900e-01;InbreedingCoeff=7.38000e-02;MQ=5.93900e+01;MQ0=0;MQRankSum=1.20610e+01;QD=3.46800e+01;ReadPosRankSum=7.92100e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487214;VQSLOD=6.35000e-01;culprit=FS;CSQ=C|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs3748595|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||10/18||ENST00000327044.6:c.1192-41N>G||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674||||||||INTRON_SIZE:272||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs3748595|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||8/16||ENST00000477976.1:n.2639-41N>G||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3748595|1|2246|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.1602|C:0.78|C:0.86|C:0.86|C:0.85|C:0.831139|C:0.932674||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,44:44:99:1706,132,0 1/1:0,43:43:99:1773,129,0 1/1:0,41:41:99:1582,123,0 1/1:0,19:19:54:687,54,0 1/1:0,23:23:69:851,69,0 1/1:0,10:10:30:370,30,0 1/1:0,33:33:99:1320,99,0 1/1:1,25:25:75:1020,75,0 1/1:0,26:26:78:1040,78,0 1/1:0,25:25:75:1000,75,0 1/1:0,36:36:99:1461,108,0 0/1:23,14:36:99:439,0,642 1/1:0,23:23:69:930,69,0 1/1:0,28:28:84:1121,84,0 1/1:0,23:23:69:904,69,0 1/1:0,37:37:99:1420,108,0 +1 887801 rs3828047 A G 1348829.24 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=4.41560e+01;DB;DP=777;Dels=0.00000e+00;FS=8.43510e+01;HaplotypeScore=3.07000e-01;InbreedingCoeff=-1.77000e-02;MQ=5.58800e+01;MQ0=35;MQRankSum=-2.15910e+01;QD=3.44400e+01;ReadPosRankSum=5.44300e+00;SNPEFF_AMINO_ACID_CHANGE=T394;SNPEFF_CODON_CHANGE=acT/acC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_887792_887980;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=-6.22100e-01;culprit=MQ;CSQ=G|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1232|1182|394|T|acT/acC|rs3828047&COSM426785|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|||10/19||Pfam_domain:PF03715&Superfamily_domains:SSF48371|ENST00000327044.6:c.1182N>C|ENST00000327044.6:c.1182N>C(p.%3D)|A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1||||||POSITION:0.525333333333333||NON_CAN_SPLICE_SURR&ANC_ALLELE|||||||,G|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2629|||||rs3828047&COSM426785|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||8/17|||ENST00000477976.1:n.2629N>C||A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1|||||||||||||||,G|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3828047&COSM426785|1|2005|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0716|G:0.90|G:0.92|G:0.92|G:0.95|G:0.906037|G:0.938372||0&1||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,42:42:99:1553,126,0 1/1:0,48:48:99:1824,138,0 1/1:0,54:54:99:1997,163,0 1/1:0,17:18:48:615,48,0 1/1:0,33:33:99:1220,99,0 1/1:0,30:30:90:1134,90,0 1/1:0,60:60:99:2315,181,0 1/1:0,44:44:99:1526,120,0 1/1:0,71:71:99:2791,214,0 1/1:0,48:48:99:1887,144,0 1/1:0,61:61:99:2398,184,0 0/1:29,33:59:99:915,0,742 1/1:0,30:30:90:1157,90,0 1/1:0,59:59:99:2321,178,0 1/1:0,55:55:99:2137,166,0 1/1:0,65:65:99:2507,196,0 +1 888529 . G A 1833.13 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-9.33700e+00;DP=387;Dels=0.00000e+00;FS=8.33000e-01;HaplotypeScore=1.94900e-01;InbreedingCoeff=-4.20000e-03;MQ=5.60200e+01;MQ0=0;MQRankSum=5.49600e+00;QD=1.10400e+01;ReadPosRankSum=-2.04000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487214;VQSLOD=1.38000e+00;culprit=MQ;CSQ=A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs373469542|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||9/18||ENST00000327044.6:c.1002+26N>T|||||||A:0.000908|A:0||||||||INTRON_SIZE:574||NON_CAN_SPLICE|||||||,A|ENSG00000188976|ENST00000477976|Transcript|intron_variant&non_coding_transcript_variant||||||rs373469542|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||7/16||ENST00000477976.1:n.2449+26N>T|||||||A:0.000908|A:0|||||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs373469542|1|1277|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||A:0.000908|A:0||||||||||||||||| GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,703 0/0:26,0:26:78:0,78,1022 0/0:23,0:23:69:0,69,869 0/0:15,0:15:45:0,45,555 0/0:16,0:16:48:0,48,603 0/0:16,0:16:48:0,48,606 0/0:32,0:32:96:0,96,1258 0/0:26,0:26:72:0,72,944 0/0:24,0:24:69:0,69,898 0/1:12,15:26:99:432,0,321 0/0:31,0:31:93:0,93,1240 0/0:24,0:24:72:0,72,944 0/0:20,0:20:60:0,60,756 0/0:27,0:27:78:0,78,1029 0/0:36,0:36:99:0,108,1415 0/0:26,0:26:78:0,78,1022 +1 888659 rs3748597 T C 907727.36 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=4.09230e+01;DB;DP=542;Dels=0.00000e+00;FS=4.67910e+01;HaplotypeScore=2.81100e-01;InbreedingCoeff=-1.65000e-02;MQ=5.48600e+01;MQ0=44;MQRankSum=-2.23740e+01;QD=3.38200e+01;ReadPosRankSum=8.50400e+00;SNPEFF_AMINO_ACID_CHANGE=I300V;SNPEFF_CODON_CHANGE=Atc/Gtc;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_888555_888668;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=-6.49600e-01;culprit=MQ;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs3748597|1|4967|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|missense_variant|948|898|300|I/V|Atc/Gtc|rs3748597|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|tolerated(0.98)|benign(0)|9/19||Superfamily_domains:SSF48371|ENST00000327044.6:c.898N>G|ENSP00000317992.6:p.Ile300Val|T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372||||||||POSITION:0.399111111111111||NON_CAN_SPLICE_SURR&ANC_ALLELE||B|0.940|P|T|T|T,C|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2345|||||rs3748597|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||7/17|||ENST00000477976.1:n.2345N>G||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3748597|1|1147|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0716|C:0.90|C:0.92|C:0.92|C:0.95|C:0.905767|C:0.938372||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,33:33:96:1198,96,0 1/1:0,29:29:87:1140,87,0 1/1:0,27:27:81:998,81,0 1/1:0,27:27:81:962,81,0 1/1:0,19:19:57:686,57,0 1/1:0,22:22:63:796,63,0 1/1:0,39:39:99:1474,117,0 1/1:0,39:39:99:1504,117,0 1/1:0,32:32:96:1183,96,0 1/1:0,44:44:99:1654,129,0 1/1:0,55:55:99:2079,166,0 0/1:17,21:36:99:502,0,410 1/1:0,37:37:99:1398,111,0 1/1:0,44:44:99:1697,132,0 1/1:0,32:32:96:1209,96,0 1/1:0,27:27:81:1016,81,0 +1 889158 rs56262069 G C 909575.03 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=3.68810e+01;DB;DP=579;Dels=0.00000e+00;FS=2.80669e+02;HaplotypeScore=5.39300e-01;InbreedingCoeff=7.80000e-02;MQ=5.90100e+01;MQ0=0;MQRankSum=-1.97700e+00;QD=3.19700e+01;ReadPosRankSum=8.43100e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000469563;VQSLOD=9.10000e-02;culprit=MQRankSum;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs13303056|1|4468|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1529|||||||||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|splice_region_variant&intron_variant||||||rs13303056|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||8/18||ENST00000327044.6:c.888+4N>G||G:0.1529||||||||||||||INTRON_SIZE:493||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant||||||rs13303056|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||6/16||ENST00000477976.1:n.2335+4N>G||G:0.1529|||||||||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs13303056|1|648|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||G:0.1529||||||||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,45:45:99:1664,135,0 1/1:0,21:21:63:810,63,0 1/1:0,27:27:81:975,81,0 1/1:0,19:18:51:638,51,0 1/1:0,20:20:60:700,60,0 1/1:0,18:18:54:635,54,0 1/1:0,40:40:99:1512,120,0 1/1:0,34:34:99:1312,102,0 1/1:0,45:45:99:1615,132,0 1/1:0,40:40:99:1543,120,0 1/1:0,62:62:99:2392,187,0 0/1:23,19:40:99:499,0,598 1/1:0,45:45:99:1664,135,0 1/1:0,48:48:99:1814,144,0 1/1:0,39:39:99:1503,117,0 1/1:0,37:37:99:1398,111,0 +1 889159 rs13302945 A C 937927.21 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=5.17190e+01;DB;DP=586;Dels=0.00000e+00;FS=2.49622e+02;HaplotypeScore=5.35000e-01;InbreedingCoeff=7.77000e-02;MQ=5.90200e+01;MQ0=0;MQRankSum=1.48040e+01;QD=3.22600e+01;ReadPosRankSum=8.79200e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000469563;VQSLOD=1.40000e-01;culprit=MQ;CSQ=C|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs13302945|1|4467|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|splice_region_variant&intron_variant||||||rs13302945|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||8/18||ENST00000327044.6:c.888+3N>G||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294||||||||INTRON_SIZE:493||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant||||||rs13302945|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||6/16||ENST00000477976.1:n.2335+3N>G||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs13302945|1|647|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.1538|C:0.79|C:0.87|C:0.88|C:0.85|C:0.823342|C:0.932294||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,44:44:99:1663,132,0 1/1:0,21:21:63:794,63,0 1/1:0,28:28:84:1058,84,0 1/1:0,19:18:51:634,51,0 1/1:0,21:21:63:782,63,0 1/1:0,18:18:54:650,54,0 1/1:0,42:42:99:1587,126,0 1/1:0,34:34:99:1312,102,0 1/1:0,45:45:99:1657,132,0 1/1:0,41:41:99:1582,123,0 1/1:0,61:61:99:2353,184,0 0/1:24,19:41:99:482,0,633 1/1:0,43:43:99:1625,129,0 1/1:0,52:52:99:1965,156,0 1/1:0,42:42:99:1557,123,0 1/1:0,35:35:99:1323,105,0 +1 889238 rs3828049 G A 52801.55 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-4.91500e+00;DB;DP=911;Dels=0.00000e+00;FS=4.16200e+01;HaplotypeScore=2.87900e-01;InbreedingCoeff=3.34000e-02;MQ=5.93400e+01;MQ0=1;MQRankSum=3.62800e+00;QD=1.41200e+01;ReadPosRankSum=-2.71000e+00;SNPEFF_AMINO_ACID_CHANGE=A271V;SNPEFF_CODON_CHANGE=gCg/gTg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_889162_889272;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=5.38000e+00;culprit=MQRankSum;CSQ=A|ENSG00000188976|ENST00000469563|Transcript|downstream_gene_variant||||||rs3828049&COSM1602748|1|4388|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1|||||||||||||||,A|ENSG00000188976|ENST00000327044|Transcript|missense_variant|862|812|271|A/V|gCg/gTg|rs3828049&COSM1602748|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C|deleterious(0.04)|benign(0.034)|8/19||Superfamily_domains:SSF48371|ENST00000327044.6:c.812N>T|ENSP00000317992.6:p.Ala271Val|A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1||||||POSITION:0.360888888888889||NON_CAN_SPLICE_SURR||D%3BP%3BP|21.3|N|T|D|T,A|ENSG00000188976|ENST00000477976|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2259|||||rs3828049&COSM1602748|1||-1|NOC2L|HGNC|24517|retained_intron||||||||||6/17|||ENST00000477976.1:n.2259N>T||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1|||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|downstream_gene_variant||||||rs3828049&COSM1602748|1|568|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||A:0.0537|A:0.02|A:0.08|A:0.08|A:0.05|A:0.021562|A:0.060363||0&1||||||||||||||| GT:AD:DP:GQ:PL 0/0:53,0:53:99:0,159,1960 0/0:56,0:56:99:0,169,2071 0/0:42,0:42:99:0,126,1517 0/0:23,0:23:69:0,69,763 0/0:31,0:31:93:0,93,1007 0/0:26,0:26:69:0,69,754 0/0:55,0:55:99:0,166,1987 0/0:59,0:59:99:0,178,2132 0/0:67,0:67:99:0,202,2362 0/0:79,0:79:99:0,238,2854 0/0:82,0:82:99:0,247,2963 0/1:32,31:62:99:888,0,808 0/0:75,0:75:99:0,226,2644 0/0:66,0:66:99:0,199,2385 0/0:68,0:68:99:0,205,2397 0/0:67,0:67:99:0,202,2362 +1 894573 rs13303010 G A 310883.38 PASS AC=30;AF=9.38000e-01;AN=32;BaseQRankSum=1.22670e+01;DB;DP=304;Dels=0.00000e+00;FS=2.34720e+01;HaplotypeScore=3.24800e-01;InbreedingCoeff=4.23300e-01;MQ=5.89800e+01;MQ0=0;MQRankSum=1.80380e+01;QD=2.67400e+01;ReadPosRankSum=2.89300e+00;SNPEFF_EFFECT=INTRON;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VQSLOD=1.10000e+00;culprit=MQ;CSQ=A|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant||||||rs13303010|1|3534|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000327044|Transcript|intron_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||1/18||ENST00000327044.6:c.26+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||INTRON_SIZE:133||NON_CAN_SPLICE|||||||,A|ENSG00000187961|ENST00000338591|Transcript|upstream_gene_variant||||||rs13303010|1|1394|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|upstream_gene_variant||||||rs13303010|1|2256|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000469563|Transcript|intron_variant&non_coding_transcript_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|retained_intron|||||||||||1/1||ENST00000469563.1:n.42+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs13303010|1|735|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs13303010|1|4359|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A|ENSG00000188976|ENST00000487214|Transcript|intron_variant&non_coding_transcript_variant||||||rs13303010|1||-1|NOC2L|HGNC|24517|processed_transcript|||||||||||1/6||ENST00000487214.1:n.95+22N>T||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942|||||||||||||||||,A||ENSR00000528861|RegulatoryFeature|regulatory_region_variant||||||rs13303010|1||||||regulatory_region|||||||||||||||G:0.3480|A:0.18|A:0.71|A:0.69|A:0.90|A:0.284570|A:0.896942||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,24:24:72:898,72,0 0/1:10,8:17:99:196,0,291 1/1:0,13:12:36:454,36,0 1/1:0,7:7:21:254,21,0 1/1:0,5:5:15:181,15,0 1/1:0,13:13:36:428,36,0 1/1:0,31:31:93:1120,93,0 1/1:0,24:24:72:867,72,0 1/1:0,26:26:78:924,78,0 1/1:0,26:26:78:958,78,0 1/1:0,19:19:57:670,57,0 0/1:17,6:22:99:127,0,513 1/1:0,20:20:60:723,60,0 1/1:0,23:23:69:869,69,0 1/1:0,19:19:57:686,57,0 1/1:0,16:16:48:505,48,0 +1 896922 . C T 1253.52 PASS AC=2;AF=6.30000e-02;AN=32;BaseQRankSum=-8.14600e+00;DP=943;Dels=0.00000e+00;FS=5.89500e+00;HaplotypeScore=1.37200e-01;InbreedingCoeff=-1.30000e-03;MQ=5.92800e+01;MQ0=0;MQRankSum=1.05600e+00;QD=1.01100e+01;ReadPosRankSum=-1.19000e+00;SNPEFF_AMINO_ACID_CHANGE=A119;SNPEFF_CODON_CHANGE=gcC/gcT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_896673_896932;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=8.89000e+00;culprit=InbreedingCoeff;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant|||||||1|1185|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant|||||||1|2252|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|464|357|119|A|gcC/gcT||1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||2/12||Pfam_domain:PF00651&PROSITE_profiles:PS50097&SMART_domains:SM00225&Superfamily_domains:SSF54695&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.357N>T|ENST00000338591.3:c.357N>T(p.%3D)|||||||||||||||POSITION:0.1850699844479||NON_CAN_SPLICE_SURR|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant|||||||1|4960|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|94||||||1||1|KLHL17|HGNC|24023|retained_intron||||||||||1/2|||ENST00000463212.1:n.94N>T|||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant|||||||1|4960|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant|||||||1|2286|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant|||||||1|4955|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant|||||||1|3084|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant|||||||1|2010|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant|||||||1|2233|-1|NOC2L|HGNC|24517|processed_transcript||||||||||||||||||||||||||||||||||||||,T||ENSR00000528861|RegulatoryFeature|regulatory_region_variant|||||||1||||||regulatory_region|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:71,0:71:99:0,214,2684 0/0:69,0:69:99:0,208,2713 0/0:68,0:68:99:0,205,2515 0/0:20,0:20:57:0,57,722 0/0:29,0:29:87:0,87,1096 0/0:36,0:36:99:0,99,1225 0/0:61,0:61:99:0,184,2353 0/0:58,0:58:99:0,175,2192 0/0:68,0:68:99:0,205,2673 0/1:41,25:63:99:678,0,1190 0/0:87,0:87:99:0,262,3356 0/0:52,0:52:99:0,157,2006 0/1:35,23:55:99:651,0,922 0/0:79,0:79:99:0,238,3048 0/0:73,0:73:99:0,220,2816 0/0:54,0:54:99:0,163,2045 +1 897325 rs4970441 G C 2226684.78 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=3.69960e+01;DB;DP=1475;Dels=0.00000e+00;FS=1.12830e+01;HaplotypeScore=4.66400e-01;InbreedingCoeff=1.15000e-01;MQ=5.95500e+01;MQ0=1;MQRankSum=2.60000e-02;QD=3.33700e+01;ReadPosRankSum=6.38900e+00;SNPEFF_AMINO_ACID_CHANGE=A203;SNPEFF_CODON_CHANGE=gcG/gcC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_897206_897427;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=5.29000e+00;culprit=ReadPosRankSum;CSQ=C|ENSG00000187961|ENST00000466300|Transcript|upstream_gene_variant||||||rs4970441|1|782|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs4970441|1|2655|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|716|609|203|A|gcG/gcC|rs4970441|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||4/12||Pfam_domain:PF07707&SMART_domains:SM00875&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.609N>C|ENST00000338591.3:c.609N>C(p.%3D)|G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||POSITION:0.315707620528771||NON_CAN_SPLICE_SURR|||||||,C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs4970441|1|4557|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|422|||||rs4970441|1||1|KLHL17|HGNC|24023|retained_intron||||||||||2/2|||ENST00000463212.1:n.422N>C||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs4970441|1|4557|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs4970441|1|2689|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs4970441|1|4552|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs4970441|1|3487|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs4970441|1|1607|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs4970441|1|2636|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||G:0.1276|C:0.71|C:0.88|C:0.92|C:0.94|C:0.727520|C:0.926163||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,94:94:99:3476,283,0 1/1:0,87:87:99:3356,262,0 1/1:0,108:108:99:3994,325,0 1/1:0,56:56:99:2023,169,0 1/1:0,59:59:99:2182,178,0 1/1:0,46:46:99:1701,138,0 1/1:0,100:100:99:3780,301,0 1/1:0,127:127:99:4800,382,0 1/1:0,127:127:99:4899,382,0 1/1:0,127:127:99:4800,382,0 1/1:0,117:117:99:4422,352,0 0/1:42,33:71:99:891,0,1116 1/1:0,78:78:99:2948,235,0 1/1:0,107:107:99:4128,322,0 1/1:0,95:95:99:3665,286,0 1/1:0,76:76:99:2873,229,0 +1 898313 . C T 4423.71 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=1.00100e+01;DP=235;Dels=0.00000e+00;FS=6.83200e+00;HaplotypeScore=5.07500e-01;InbreedingCoeff=9.84000e-02;MQ=5.92600e+01;MQ0=0;MQRankSum=-5.62000e-01;QD=1.22500e+01;ReadPosRankSum=-4.59200e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=3.67000e+00;culprit=MQRankSum;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|intron_variant&NMD_transcript_variant||||||rs375277853|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||1/5||ENST00000466300.1:c.191+16N>T|||||||||||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs375277853|1|3643|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs375277853|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1042+16N>T||||||||||||||||INTRON_SIZE:191||NON_CAN_SPLICE|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs375277853|1|3569|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs375277853|1|455|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs375277853|1|3569|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs375277853|1|3677|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs375277853|1|3564|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||||||||||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs375277853|1|4475|-1|NOC2L|HGNC|24517|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs375277853|1|619|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||||||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs375277853|1|3624|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,653 0/0:12,0:12:36:0,36,423 0/0:21,0:21:63:0,63,740 0/0:6,0:6:15:0,15,157 0/0:2,0:2:6:0,6,63 0/0:6,0:6:15:0,15,159 0/0:14,0:14:42:0,42,455 0/0:18,0:18:54:0,54,624 0/0:14,0:14:39:0,39,447 0/0:25,0:25:72:0,72,805 0/0:16,0:16:48:0,48,564 0/1:13,8:20:99:190,0,314 0/0:21,0:21:63:0,63,702 0/0:17,1:18:18:0,18,560 0/0:11,0:11:30:0,30,342 0/0:12,0:12:36:0,36,393 +1 898323 rs6605071 T C 353673.96 PASS AC=31;AF=9.69000e-01;AN=32;BaseQRankSum=1.91890e+01;DB;DP=221;Dels=0.00000e+00;FS=9.64600e+00;HaplotypeScore=4.04000e-01;InbreedingCoeff=-2.15000e-02;MQ=5.91700e+01;MQ0=0;MQRankSum=-4.60000e-02;QD=3.77900e+01;ReadPosRankSum=3.36900e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=4.11000e+00;culprit=InbreedingCoeff;CSQ=C|ENSG00000187961|ENST00000466300|Transcript|intron_variant&NMD_transcript_variant||||||rs6605071|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||1/5||ENST00000466300.1:c.191+26N>C||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs6605071|1|3653|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs6605071|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1042+26N>C||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||INTRON_SIZE:191||NON_CAN_SPLICE&ANC_ALLELE|||||||,C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs6605071|1|3559|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs6605071|1|465|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs6605071|1|3559|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs6605071|1|3687|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs6605071|1|3554|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||EXON_INTRON_UNDEF&ANC_ALLELE|||||||,C|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs6605071|1|4485|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs6605071|1|609|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859|||||||||||||||||,C|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs6605071|1|3634|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0725|C:0.92|C:0.91|C:0.92|C:0.95|C:0.926218|C:0.940859||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,18:18:54:688,54,0 1/1:0,8:8:24:315,24,0 1/1:0,15:15:45:579,45,0 1/1:0,7:7:21:262,21,0 1/1:0,3:3:9:111,9,0 1/1:0,4:4:9:122,9,0 1/1:0,20:20:60:786,60,0 1/1:0,16:16:48:641,48,0 1/1:0,13:13:36:457,36,0 1/1:0,27:27:78:1030,78,0 1/1:0,18:18:54:720,54,0 0/1:13,4:17:99:112,0,396 1/1:0,18:18:54:708,54,0 1/1:0,13:13:39:525,39,0 1/1:0,10:10:30:393,30,0 1/1:1,13:14:5:460,5,0 +1 898467 rs41285808 C T 14490.29 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-2.26300e+00;DB;DP=270;Dels=0.00000e+00;FS=1.33000e+00;HaplotypeScore=2.81700e-01;InbreedingCoeff=3.75000e-02;MQ=5.93000e+01;MQ0=0;MQRankSum=3.96000e+00;QD=1.37100e+01;ReadPosRankSum=-1.57400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;VQSLOD=7.17000e+00;culprit=FS;CSQ=T|ENSG00000187961|ENST00000466300|Transcript|synonymous_variant&NMD_transcript_variant|247|249|83|P|ccC/ccT|rs41285808|1||1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||2/6|||ENST00000466300.1:c.247N>T|ENST00000466300.1:c.247N>T(p.%3D)|T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000188976|ENST00000327044|Transcript|upstream_gene_variant||||||rs41285808|1|3797|-1|NOC2L|HGNC|24517|protein_coding|YES||CCDS3.1|ENSP00000317992|NOC2L_HUMAN||UPI000041820C||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||rs41285808|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||6/11||ENST00000338591.3:c.1043-22N>T||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||INTRON_SIZE:191||NON_CAN_SPLICE|||||||,T|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs41285808|1|3415|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs41285808|1|609|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs41285808|1|3415|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000469563|Transcript|upstream_gene_variant||||||rs41285808|1|3831|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs41285808|1|3410|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||EXON_INTRON_UNDEF|||||||,T|ENSG00000188976|ENST00000477976|Transcript|upstream_gene_variant||||||rs41285808|1|4629|-1|NOC2L|HGNC|24517|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000187961|ENST00000481067|Transcript|upstream_gene_variant||||||rs41285808|1|465|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672|||||||||||||||||,T|ENSG00000188976|ENST00000487214|Transcript|upstream_gene_variant||||||rs41285808|1|3778|-1|NOC2L|HGNC|24517|processed_transcript|||||||||||||||T:0.0500|T:0.0020|T:0.08|T:0.08|T:0.05|T:0.010512|T:0.056672||||||||||||||||| GT:AD:DP:GQ:PL 0/0:28,0:28:84:0,84,1030 0/0:15,0:15:45:0,45,579 0/0:25,0:25:75:0,75,916 0/0:6,0:6:18:0,18,197 0/0:5,0:5:15:0,15,172 0/0:3,0:3:9:0,9,100 0/0:14,0:14:42:0,42,480 0/0:22,0:22:66:0,66,817 0/0:23,0:23:69:0,69,831 0/0:12,0:12:36:0,36,431 0/0:18,0:18:51:0,51,646 0/1:17,10:26:99:278,0,440 0/0:21,0:21:51:0,51,644 0/0:13,0:13:39:0,39,481 0/0:18,0:18:54:0,54,666 0/0:21,0:21:60:0,60,723 +1 899959 . G GC 2073.57 PASS AC=1;AF=5.00000e-02;AN=20;BaseQRankSum=8.77000e-01;DP=19;FS=1.24470e+02;HaplotypeScore=1.51273e+01;InbreedingCoeff=6.94000e-02;MQ=4.52200e+01;MQ0=0;MQRankSum=-8.47500e+00;QD=1.40100e+01;ReadPosRankSum=4.26000e-01;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000463212;CSQ=C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1922|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|2101|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1922|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|49|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E|||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||TMP_ESP_1_899960_899959|1|1917|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|||||||||||||C:0.152075|C:0.090390||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||TMP_ESP_1_899960_899959|1|415|1|KLHL17|HGNC|24023|retained_intron||||||||||||||||||||C:0.152075|C:0.090390|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|intron_variant||||||TMP_ESP_1_899960_899959|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||11/11||ENST00000338591.3:c.1700+49_1700+50insC|||||||C:0.152075|C:0.090390||||||||INTRON_SIZE:432||NON_CAN_SPLICE||||||| GT:AD:DP:GQ:PL ./.:.:.:.:. ./.:.:.:.:. 0/0:3,0:3:9:0,9,136 0/0:1,0:1:3:0,3,45 0/0:1,0:1:3:0,3,45 0/0:2,0:2:6:0,6,91 0/1:3,1:4:28:28,0,124 0/0:2,0:2:6:0,6,74 0/0:2,0:2:6:0,6,91 0/0:2,0:2:6:0,6,91 ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. 0/0:1,0:1:3:0,3,45 ./.:.:.:.:. 0/0:1,0:1:3:0,3,45 +1 900505 rs28705211 G C 222602.28 PASS AC=8;AF=2.50000e-01;AN=32;BaseQRankSum=6.97200e+00;DB;DP=885;Dels=0.00000e+00;FS=4.61940e+01;HaplotypeScore=1.18840e+00;InbreedingCoeff=1.98200e-01;MQ=5.92300e+01;MQ0=0;MQRankSum=1.76580e+01;QD=1.80400e+01;ReadPosRankSum=1.01980e+01;SNPEFF_AMINO_ACID_CHANGE=V497;SNPEFF_CODON_CHANGE=gtG/gtC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_900343_901094;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000455747;VQSLOD=1.37000e+00;culprit=HaplotypeScore;CSQ=C|ENSG00000187583|ENST00000379409|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1377|1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|2647|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187583|ENST00000379407|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1377|1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|595|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|upstream_gene_variant||||||rs28705211&COSM426805|1|1372|1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs28705211&COSM426805|1|961|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|synonymous_variant|1970|1863|621|V|gtG/gtC|rs28705211&COSM426805|1||1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0|||12/12||SMART_domains:SM00612&Superfamily_domains:SSF117281&PIRSF_domain:PIRSF037037|ENST00000338591.3:c.1863N>C|ENST00000338591.3:c.1863N>C(p.%3D)|C:0.1648|C:0.02|C:0.22|C:0.09|C:0.28||||0&1|20637081|||||POSITION:0.965785381026439||END_TRUNC&NON_CAN_SPLICE_SURR||||||| GT:AD:DP:GQ:PL 0/0:87,0:87:99:0,262,3217 0/1:43,24:61:99:697,0,1146 0/1:35,29:60:99:812,0,913 0/0:23,0:23:69:0,69,851 0/0:22,0:22:66:0,66,788 0/0:33,1:34:96:0,96,1150 0/0:54,0:54:99:0,162,1973 0/1:32,27:56:99:720,0,880 0/0:79,0:79:99:0,235,2850 0/0:74,0:74:99:0,214,2587 0/0:65,0:65:99:0,196,2354 0/1:24,26:48:99:738,0,687 0/1:27,28:54:99:795,0,709 0/0:58,0:58:99:0,175,2173 0/1:28,27:54:99:805,0,735 1/1:0,56:56:99:2066,169,0 +1 902024 rs181910588 G 406.47 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-3.35500e+00;DB;DP=225;Dels=0.00000e+00;FS=1.03150e+01;HaplotypeScore=3.56800e-01;InbreedingCoeff=-1.33000e-02;MQ=5.93500e+01;MQ0=0;MQRankSum=1.21200e+00;QD=1.09900e+01;ReadPosRankSum=-1.50700e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=6.64000e+00;culprit=InbreedingCoeff;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs181910588|1|4231|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs181910588|1|2114|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs181910588|1|929|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs181910588|1|4166|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs181910588|1|2480|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs181910588|1||||||regulatory_region|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||||||||| GT:AD:DP:GQ:PL 0/0:18,0:18:54:0,54,689 0/0:21,0:21:63:0,63,797 0/0:17,0:17:48:0,48,608 0/0:5,0:5:15:0,15,182 0/0:9,0:9:27:0,27,333 0/0:7,0:7:21:0,21,253 0/0:18,0:18:54:0,54,680 0/0:7,0:7:21:0,21,259 0/0:17,0:17:51:0,51,614 0/0:19,0:19:54:0,54,647 0/0:20,0:20:60:0,60,756 0/0:14,0:14:42:0,42,518 0/0:13,0:13:36:0,36,466 0/0:14,0:14:42:0,42,535 0/1:9,1:11:4:4,0,296 0/0:15,0:15:45:0,45,551 +1 902069 rs116147894 T C 13024.04 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=2.08840e+01;DB;DP=157;Dels=0.00000e+00;FS=3.07700e+00;HaplotypeScore=2.10500e-01;InbreedingCoeff=1.00200e-01;MQ=5.91800e+01;MQ0=0;MQRankSum=7.75000e-01;QD=1.56200e+01;ReadPosRankSum=-5.68400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=7.17000e+00;culprit=MQ;CSQ=C|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs116147894|1|4186|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs116147894|1|2159|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs116147894|1|974|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs116147894|1|4211|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs116147894|1|2525|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs116147894|1||||||regulatory_region|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||||||||| GT:AD:DP:GQ:PL 0/0:10,0:10:30:0,30,367 0/1:12,2:13:3:3,0,418 0/0:14,0:14:42:0,42,514 0/0:4,0:4:12:0,12,144 0/0:5,0:5:15:0,15,176 0/0:4,0:4:12:0,12,145 0/0:17,0:17:48:0,48,603 0/0:6,0:6:18:0,18,227 0/0:10,0:10:30:0,30,361 0/0:10,0:10:30:0,30,372 0/0:12,0:12:36:0,36,434 0/0:7,0:7:21:0,21,259 0/0:7,0:7:21:0,21,255 0/0:11,0:11:30:0,30,375 0/0:12,0:12:36:0,36,426 0/0:15,0:15:45:0,45,530 +1 902088 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 +1 902088 . G A 111 - AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 +GL000207.1 1 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 diff --git a/v03_pipeline/var/test/reference_data/test_gnomad_coding_noncoding_crdq_1.ht/.README.txt.crc b/v03_pipeline/var/test/reference_data/test_gnomad_coding_noncoding_crdq_1.ht/.README.txt.crc new file mode 100644 index 000000000..ab521f2a7 Binary files /dev/null and b/v03_pipeline/var/test/reference_data/test_gnomad_coding_noncoding_crdq_1.ht/.README.txt.crc differ diff --git a/v03_pipeline/var/test/reference_data/test_gnomad_coding_noncoding_crdq_1.ht/._SUCCESS.crc b/v03_pipeline/var/test/reference_data/test_gnomad_coding_noncoding_crdq_1.ht/._SUCCESS.crc new file mode 100644 index 000000000..3b7b04493 Binary 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