nMutataionRate in Somatic Hyper Mutation tree

[singhd6]

Hi, I generated the SHMT trees with following commands for mouse BCR sequencing:
#Find alleles#
mixcr findAlleles
--report "/mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/Pan-pan2S12/SHMT_PAN-PAN2/PANPAN2.findAlleles.report.txt"
--export-alleles-mutations "/mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/Pan-pan2S12/SHMT_PAN-PAN2/PANPAN2/PANPAN2_Alleles.tsv"
--export-library "/mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/Pan-pan2S12/SHMT_PAN-PAN2/PANPAN2/PANPAN2_Alleles.json"
--output-template "/mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/Pan-pan2S12/result2/Pan-pan2.reassigned.clns"
"/mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/Pan-pan2S12/result2/Pan-pan2S12.clns"

#Export the reassigned .clns in .shmt format#
mixcr findShmTrees
--report "/mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/Pan-pan2S12/PAN-PAN2/PANPAN2_trees.log"
"/mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/Pan-pan2S12/result2/Pan-pan2.reassigned.clns"
"/mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/Pan-pan2S12/SHMT_PAN-PAN2/PANPAN2.shmt"
#export SHM trees with nodes#
mixcr exportShmTreesWithNodes
"/mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/Pan-pan2S12/SHMT_PAN-PAN2/PANPAN2.shmt"
"/mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/Pan-pan2S12/SHMT_PAN-PAN2/PANPAN2_Trees.tsv"

I am trying to understand the somatic hypermutation trees:
treeId nodeId isObserved chains parentId DistanceFromGermline nMutationsRate cloneId fileName readCount readFraction targetSequences targetQualities bestVHit bestDHit bestJHit bestCHit allVAlignments allDAlignments allJAlignments allCAlignments nSeqFR1 nSeqCDR1 nSeqFR2 nSeqCDR2 nSeqFR3 nSeqCDR3 nSeqFR4 aaSeqFR1 aaSeqCDR1 aaSeqFR2 aaSeqCDR2 aaSeqFR3 aaSeqCDR3 aaSeqFR4 isotype refPoints
74 14 TRUE IGH 4 132 0.390532544 3233 /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/JA10S1/JA10SHMT/JA10.reassigned.clns 124 2.88E-05 CTAGAATGGATTGGAGAAATTAATCCAGATAGCAGTACGATAAACTATACGCCATCTCTAAAGGATAAATTCATCATCTCCAGAGACAACGCCAAAAATACGCTGTACCTGCAAATGAGCAAAGTGAGATCTGAGGACACAGCCCTTTATTACTGTGCAAGTATCTATGATGGTTACTTCCACTTTGACTACTGGGGCCAAGGCACCACTCTCACAGTCTCCTCAG NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN IGHV4-100-M8-5OIS4G6YYQRS2JEG37HKSY5G IGHD2-300 IGHJ200 IGHM00 74|367|388|0|161|DG74DA75DG76DG77DT78DG79DA80DA81DG82DC83DT84DT85DC86DT87DC88DG89DA90DG91DT92DC93DT94DG95DG96DA97DG98DG99DT100DG101DG102DC103DC104DT105DG106DG107DT108DG109DC110DA111DG112DC113DC114DT115DG116DG117DA118DG119DG120DA121DT122DC123DC124DC125DT126DG127DA128DA129DA130DC131DT132DC133DT134DC135DC136DT137DG138DT139DG140DC141DA142DG143DC144DC145DT146DC147DA148DG149DG150DA151DT152DT153DC154DG155DA156DT157DT158DT159DT160DA161DG162DT163DA164DG165DA166DT167DA168DC169DT170DG171DG172DA173DT174DG175DA176DG177DT178DT179DG180DG181DG182DT183DC184DC185DG186DG187DC188DA189DG190DG191DC192DT193DC194DC195DA196DG197DG198DG199DA200DA201DA202DG203DG204DG205|107.0 16|32|51|162|178||80.0 23|68|68|181|226||450.0 CTAGAATGGATTGGAGAA ATTAATCCAGATAGCAGTACGATA AACTATACGCCATCTCTAAAGGATAAATTCATCATCTCCAGAGACAACGCCAAAAATACGCTGTACCTGCAAATGAGCAAAGTGAGATCTGAGGACACAGCCCTTTATTAC TGTGCAAGTATCTATGATGGTTACTTCCACTTTGACTACTGG GGCCAAGGCACCACTCTCACAGTCTCCTCAG LEWIGE INPDSSTI NYTPSLKDKFIISRDNAKNTLYLQMSKVRSEDTALYY CASIYDGYFHFDYW GQGTTLTVSS IgM ::::0:0:0:18:42:153:-1:161:162:1:-2:178:181:-3:195:226::
"In the above tree the nMutation rate for treeID74 is 0.390532544 and distance from germline is 132, according to MIXCR documents: n mutation rate is "Number of nucleotide mutations from germline divided by target sequence size" now if i see the target sequence size of the treeID74 is 226 and i divide 132/226 = 0.584070796460177, then why the nMuatation rate is 0.390532544. Unless target sequence size is something else and how mixcr is calculating the mutation rate i want to understand. I calculated the total number of nucleotide from the column target sequence which is 226. Can you please explain how do you calculate the nMutation rate for somatic hypermutation tree."
Thank you
Divya

[singhd6]

Could anyone please answer my question. I am waiting for the response about the nucleotide mutation rate calculation in MIXCR/4.7.0. Thank you very much - Divya

[mizraelson]

Answered in #1967