Miltenyi Biotec TCR α/β RNA Profiling Kit, human
This kit allows to obtain TCR alpha and beta repertoires for different types of available RNA material, with high sensitivity and UMI-based accuracy.
Bellow you can see the structure of cDNA library.
The data for this tutorial consists of two samples that represent two replicas of the same biological sample. Total RNA was isolated from PBMC and 25ng were used for each cDNA synthesis. Two cDNA libraries were prepared for each sample (one for TCR alpha and one for TCR betta) according to Miltenyi Biotec TCR α/β RNA Profiling Kit, human kit protocol. TCR sequencing was performed on an Illumina Miseq sequencer using the 300-cycle Miseq reagent kit(Illumina) with pair-end, 2x150 base pair reads.
All data may be downloaded using the script bellow.
Use aria2c for efficient download of the full dataset with the proper filenames:
download.sh
mkdir -p raw
aria2c -c -s 16 -x 16 -k 1M -j 8 -i download-list.txt
download-list.txt
https://cdn.milaboratory.com/data/milab-tcr-mulriplex/Multi_TRA_FS115_1_S149_R1_001.fastq.gz
out=raw/Multi_TRA_FS115_1_R1.fastq.gz
https://cdn.milaboratory.com/data/milab-tcr-mulriplex/Multi_TRA_FS115_1_S149_R2_001.fastq.gz
out=raw/Multi_TRA_FS115_1_R2.fastq.gz
https://cdn.milaboratory.com/data/milab-tcr-mulriplex/Multi_TRA_FS115_2_S150_R1_001.fastq.gz
out=raw/Multi_TRA_FS115_2_R1.fastq.gz
https://cdn.milaboratory.com/data/milab-tcr-mulriplex/Multi_TRA_FS115_2_S150_R2_001.fastq.gz
out=raw/Multi_TRA_FS115_2_R2.fastq.gz
https://cdn.milaboratory.com/data/milab-tcr-mulriplex/Multi_TRB_FS115_1_S153_R1_001.fastq.gz
out=raw/Multi_TRB_FS115_1_R1.fastq.gz
https://cdn.milaboratory.com/data/milab-tcr-mulriplex/Multi_TRB_FS115_1_S153_R2_001.fastq.gz
out=raw/Multi_TRB_FS115_1_R2.fastq.gz
https://cdn.milaboratory.com/data/milab-tcr-mulriplex/Multi_TRB_FS115_2_S154_R1_001.fastq.gz
out=raw/Multi_TRB_FS115_2_R1.fastq.gz
https://cdn.milaboratory.com/data/milab-tcr-mulriplex/Multi_TRB_FS115_2_S154_R2_001.fastq.gz
out=raw/Multi_TRB_FS115_2_R2.fastq.gz
Upstream analysis
One-line solution
MiXCR has a dedicated preset for this protocol, thus analysing the data is as easy as:
mixcr analyze miltenyi-human-rna-tcr-profiling \
raw/Multi_TRA_FS115_1_R1.fastq.gz \
raw/Multi_TRA_FS115_1_R2.fastq.gz \
results/Multi_TRA_FS115_1
Running the command above will generate the following files:
> ls result/
# human-readable reports
Multi_TRA_FS115_1.report
# raw alignments (highly compressed binary file)
Multi_TRA_FS115_1.vdjca
# alignments with refined UMI barcode sequences
Multi_TRA_FS115_1.refined.vdjca
# TRA, TRB CDR3 clonotypes (highly compressed binary file)
Multi_TRA_FS115_1.clns
# TRA,TRB CDR3 clonotypes exported in tab-delimited txt
Multi_TRA_FS115_1.clonotypes.TRA.tsv
Multi_TRA_FS115_1.clonotypes.TRB.tsv
While .clns file holds all data and is used for downstream analysis using mixcr postanalisis, the output .txt clonotype table will contain exhaustive information about each clonotype as well:
See first 100 records from FebControl1.clones.IGH.tsv clonotype table
| cloneId | cloneCount | uniqueTagCountUMI | cloneFraction | targetSequences | targetQualities | allVHitsWithScore | allDHitsWithScore | allJHitsWithScore | allCHitsWithScore | allVAlignments | allDAlignments | allJAlignments | allCAlignments | nSeqFR1 | minQualFR1 | nSeqCDR1 | minQualCDR1 | nSeqFR2 | minQualFR2 | nSeqCDR2 | minQualCDR2 | nSeqFR3 | minQualFR3 | nSeqCDR3 | minQualCDR3 | nSeqFR4 | minQualFR4 | aaSeqFR1 | aaSeqCDR1 | aaSeqFR2 | aaSeqCDR2 | aaSeqFR3 | aaSeqCDR3 | aaSeqFR4 | refPoints |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 125484 | 1724 | 0.0456243 | TGTGCGGAGCTAGCGGGGATATCTAACTTTGGAAATGAGAAATTAACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(277.6) | nan | TRAJ48*00(315.7) | TRAC*00(64.5) | 264|269|297|0|5||25.0 | nan | 19|52|83|18|51||165.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCGGAGCTAGCGGGGATATCTAACTTTGGAAATGAGAAATTAACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAELAGISNFGNEKLTF | nan | :::::::::0:-8:5:::::18:1:51::: |
| 1 | 83058 | 1140 | 0.0301988 | TGTGCCGTGACCGTCTGGTGGGGAGCCCAGAAGCTGGTATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(292.3) | nan | TRAJ54*00(264.6) | TRAC*00(64.5) | 264|274|297|0|10||50.0 | nan | 27|49|80|20|42||110.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGTGACCGTCTGGTGGGGAGCCCAGAAGCTGGTATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVTVWWGAQKLVF | nan | :::::::::0:-3:10:::::20:-7:42::: |
| 2 | 60550 | 596 | 0.0220152 | TGTGCTGTGCTGTTTATGAACAGAGATGACAAGATCATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV3*00(253.2) | nan | TRAJ30*00(303.9) | TRAC*00(70.7) | 270|279|306|0|9||45.0 | nan | 13|46|77|9|42|SC18T|151.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGCTGTTTATGAACAGAGATGACAAGATCATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVLFMNRDDKIIF | nan | :::::::::0:-7:9:::::9:7:42::: |
| 3 | 47245 | 1101 | 0.0171777 | TGTGCAGGGAAAAGTGGCAACACAGGCAAACTAATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV25*00(273.2) | nan | TRAJ37*00(278.7) | TRAC*00(65) | 264|273|293|0|9||45.0 | nan | 26|51|82|14|39||125.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGGGAAAAGTGGCAACACAGGCAAACTAATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAGKSGNTGKLIF | nan | :::::::::0:0:9:::::14:-6:39::: |
| 4 | 43079 | 474 | 0.015663 | TGTGCTGGGAAAACTGGGGCAAACAACCTCTTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV3*00(244.6) | nan | TRAJ36*00(283.4) | TRAC*00(89.5) | 270|280|306|0|10|ST277G|36.0 | nan | 22|48|79|10|36||130.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGGGAAAACTGGGGCAAACAACCTCTTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAGKTGANNLFF | nan | :::::::::0:-6:10:::::10:-2:36::: |
| 5 | 28006 | 1059 | 0.0101826 | TGTGCTGTGAGTGATCGTTCAGGAGGAGGTGCTGACGGACTCACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-6*00(273.1) | nan | TRAJ45*00(308.5) | TRAC*00(64.6) | 270|286|304|0|16||80.0 | nan | 24|55|86|17|48||155.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGTGATCGTTCAGGAGGAGGTGCTGACGGACTCACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVSDRSGGGADGLTF | nan | :::::::::0:2:16:::::17:-4:48::: |
| 6 | 24675 | 493 | 0.0089715 | TGTGCAGCAATCAACACCGGTAACCAGTTCTATTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV23DV6*00(262.1) | nan | TRAJ49*00(273.3) | TRAC*00(83.1) | 267|280|300|0|13|SG277T|51.0 | nan | 21|45|76|12|36||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGCAATCAACACCGGTAACCAGTTCTATTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAAINTGNQFYF | nan | :::::::::0:0:13:::::12:-1:36::: |
| 7 | 24629 | 877 | 0.00895478 | TGTGCTGTGAGTGTCCCTTCAGGAGGAAGCTACATACCTACATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-6*00(258.9) | nan | TRAJ6*00(288.1) | TRAC*00(64.9) | 270|283|304|0|13||65.0 | nan | 24|51|82|18|45||135.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGTGTCCCTTCAGGAGGAAGCTACATACCTACATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVSVPSGGSYIPTF | nan | :::::::::0:-1:13:::::18:-4:45::: |
| 8 | 24116 | 955 | 0.00876826 | TGTGCTGTCGACACCGACAAGCTCATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV2*00(265.1) | nan | TRAJ34*00(253.2) | TRAC*00(101.7) | 249|260|283|0|11|SG257C|41.0 | nan | 27|47|78|10|30||100.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTCGACACCGACAAGCTCATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVDTDKLIF | nan | :::::::::0:-3:11:::::10:-7:30::: |
| 9 | 21145 | 366 | 0.00768804 | TGTGTGGTGAAATTTGGGTCTGGTTCTGCAAGGCAACTGACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-1*00(296.4) | nan | TRAJ22*00(292.8) | TRAC*00(64.6) | 261|272|294|0|11||55.0 | nan | 16|52|83|8|45|SC23GST24GI25G|140.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGTGGTGAAATTTGGGTCTGGTTCTGCAAGGCAACTGACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CVVKFGSGSARQLTF | nan | :::::::::0:-2:11:::::8:4:45::: |
| 10 | 18878 | 253 | 0.00686379 | TGTGCCGTGAAGGAGGATAGCAACTATCAGTTAATCTGG | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(298.1) | nan | TRAJ33*00(277.9) | TRAC*00(64.5) | 264|275|297|0|11||55.0 | nan | 21|46|77|14|39||125.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGTGAAGGAGGATAGCAACTATCAGTTAATCTGG | 45 | nan | nan | nan | nan | nan | nan | nan | CAVKEDSNYQLIW | nan | :::::::::0:-2:11:::::14:-1:39::: |
| 11 | 16805 | 275 | 0.00611008 | TGTGCCGTAGGGGGGGGGCCAAGCAGTGCTTCCAAGATAATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(283.7) | nan | TRAJ3*00(273.5) | TRAC*00(64.6) | 264|272|297|0|8||40.0 | nan | 27|51|82|21|45||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGTAGGGGGGGGGCCAAGCAGTGCTTCCAAGATAATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVGGGPSSASKIIF | nan | :::::::::0:-5:8:::::21:-7:45::: |
| 12 | 16598 | 457 | 0.00603481 | TGTGCTGTGGGTGCACTCTAACTTTGGAAATGAGAAATTAACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-3*00(271.1) | nan | TRAJ48*00(303.3) | TRAC*00(64.6) | 270|284|304|0|14||70.0 | nan | 22|52|83|16|46||150.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGGGTGCACTCTAACTTTGGAAATGAGAAATTAACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVGAL*L_GNEKLTF | nan | :::::::::0:0:14:::::16:-2:46::: |
| 13 | 16490 | 233 | 0.00599555 | TGTGCCCCTCGAGAGAGCTATGGTCAGAATTTTGTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV24*00(241.9) | nan | TRAJ26*00(263.8) | TRAC*00(69.5) | 267|273|297|0|6||30.0 | nan | 27|49|80|17|39||110.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCCCTCGAGAGAGCTATGGTCAGAATTTTGTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAPRESYGQNFVF | nan | :::::::::0:-4:6:::::17:-7:39::: |
| 14 | 14361 | 77 | 0.00522147 | TGCCTCGTGGGGGGGCGCGGTGGTGCTACAAACAAGCTCATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV4*00(262.7) | nan | TRAJ32*00(288.2) | TRAC*00(66.2) | 261|272|297|0|11||55.0 | nan | 28|55|86|18|45||135.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCCTCGTGGGGGGGCGCGGTGGTGCTACAAACAAGCTCATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CLVGGRGGATNKLIF | nan | :::::::::0:-5:11:::::18:-8:45::: |
| 15 | 13243 | 361 | 0.00481498 | TGTGCTAAACTTACCAGTGGCTCTAGGTTGACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV17*00(260.3) | nan | TRAJ58*00(272.8) | TRAC*00(74.2) | 264|271|297|0|7||35.0 | nan | 28|52|83|12|36||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTAAACTTACCAGTGGCTCTAGGTTGACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAKLTSGSRLTF | nan | :::::::::0:-6:7:::::12:-8:36::: |
| 16 | 12894 | 151 | 0.00468809 | TGTGCTGTGAGTGGATGGCCAGAAGCTGCTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-4*00(270.8) | nan | TRAJ16*00(257.9) | TRAC*00(101.9) | 270|283|304|0|13||65.0 | nan | 28|49|80|13|34||105.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGTGGATGGCCAGAAGCTGCTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVSGW_QKLLF | nan | :::::::::0:-1:13:::::13:-8:34::: |
| 17 | 10482 | 115 | 0.00381112 | TGTGCTGTGAGAGATACTTGGGGAAGCCAAGGAAATCTCATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV3*00(277) | nan | TRAJ42*00(276.8) | TRAC*00(64.7) | 270|284|306|0|14||70.0 | nan | 27|55|86|18|45|DA30|123.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGAGATACTTGGGGAAGCCAAGGAAATCTCATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRDTWGSQGNLIF | nan | :::::::::0:-2:14:::::18:-7:45::: |
| 18 | 9959 | 459 | 0.00362096 | TGTGCAGCCATTTCTGGTGGCTACAATAAGCTGATTTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV13-1*00(261.9) | nan | TRAJ4*00(298.3) | TRAC*00(65.5) | 267|275|300|0|8||40.0 | nan | 23|52|83|10|39||145.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGCCATTTCTGGTGGCTACAATAAGCTGATTTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAAISGGYNKLIF | nan | :::::::::0:-5:8:::::10:-3:39::: |
| 19 | 9450 | 159 | 0.0034359 | TGTGCTCTGACCGTTGGATTCAATGACATGCGCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV9-2*00(231.9) | nan | TRAJ43*00(234.5) | TRAC*00(109.7) | 267|277|301|0|10||50.0 | nan | 27|43|74|20|36||80.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTCTGACCGTTGGATTCAATGACATGCGCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CALTVGFNDMRF | nan | :::::::::0:-4:10:::::20:-7:36::: |
| 20 | 8077 | 115 | 0.00293669 | TGTGCAGGAAAGGAAACGGGGGAAACCAGTGGCTCTAGGTTGACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV27*00(267.4) | nan | TRAJ58*00(288) | TRAC*00(64.7) | 264|273|294|0|9||45.0 | nan | 25|52|83|21|48||135.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGGAAAGGAAACGGGGGAAACCAGTGGCTCTAGGTTGACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAGKETGETSGSRLTF | nan | :::::::::0:-1:9:::::21:-5:48::: |
| 21 | 8055 | 112 | 0.00292869 | TGTGCCGGGCAGGGCGGATCTGAAAAGCTGGTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(279.6) | nan | TRAJ57*00(288.2) | TRAC*00(64.5) | 264|271|297|0|7||35.0 | nan | 25|52|83|9|36||135.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGGGCAGGGCGGATCTGAAAAGCTGGTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAGQGGSEKLVF | nan | :::::::::0:-6:7:::::9:-5:36::: |
| 22 | 6582 | 162 | 0.00239313 | TGTGCTGGCCCCCCCCAGAGAGGAGGAAACAAACTCACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV35*00(265.4) | nan | TRAJ10*00(268.1) | TRAC*00(64.7) | 264|272|296|0|8||40.0 | nan | 30|53|84|19|42||115.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGGCCCCCCCCAGAGAGGAGGAAACAAACTCACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAGPPQRGGNKLTF | nan | :::::::::0:-4:8:::::19:-10:42::: |
| 23 | 6360 | 106 | 0.00231241 | TGTGTGGTGAACTAACCGGGGAGGTGGAGGCTTCAAAACTATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-1*00(302.1) | nan | TRAJ9*00(263.3) | TRAC*00(64.4) | 261|273|294|0|12||60.0 | nan | 28|50|81|24|46||110.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGTGGTGAACTAACCGGGGAGGTGGAGGCTTCAAAACTATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CVVN*PGR_GGFKTIF | nan | :::::::::0:-1:12:::::24:-8:46::: |
| 24 | 6312 | 176 | 0.00229496 | TGTGCTGTGTCGTATTCAGGAGGAGGTGCTGACGGACTCACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-3*00(246.9) | nan | TRAJ45*00(322.8) | TRAC*00(64.7) | 270|279|304|0|9||45.0 | nan | 21|55|86|11|45||170.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGTCGTATTCAGGAGGAGGTGCTGACGGACTCACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVSYSGGGADGLTF | nan | :::::::::0:-5:9:::::11:-1:45::: |
| 25 | 6036 | 274 | 0.00219461 | TGTGCAGCAAGCCGGACCCAGGGAGCCCAGAAGCTGGTATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV13-1*00(275.3) | nan | TRAJ54*00(273.4) | TRAC*00(64.7) | 267|278|300|0|11||55.0 | nan | 25|49|80|18|42||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGCAAGCCGGACCCAGGGAGCCCAGAAGCTGGTATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAASRTQGAQKLVF | nan | :::::::::0:-2:11:::::18:-5:42::: |
| 26 | 5863 | 22 | 0.00213171 | TGCCTCGTCTACAACTTCAACAAATTTTACTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV4*00(247.4) | nan | TRAJ21*00(273.8) | TRAC*00(103.9) | 261|269|297|0|8||40.0 | nan | 17|44|75|6|33|SA19C|121.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCCTCGTCTACAACTTCAACAAATTTTACTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CLVYNFNKFYF | nan | :::::::::0:-8:8:::::6:3:33::: |
| 27 | 5472 | 72 | 0.00198955 | TGTGCTGTCGGTTCTGGGGGTTACCAGAAAGTTACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV3*00(247.5) | nan | TRAJ13*00(292.3) | TRAC*00(76.9) | 270|278|306|0|8||40.0 | nan | 24|52|83|11|39||140.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTCGGTTCTGGGGGTTACCAGAAAGTTACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVGSGGYQKVTF | nan | :::::::::0:-8:8:::::11:-4:39::: |
| 28 | 4780 | 56 | 0.00173794 | TGTGCTGTGAGAGACGCGCAAGGAGGAGGTGCTGACGGACTCACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV3*00(280.8) | nan | TRAJ45*00(293.6) | TRAC*00(64.5) | 270|285|306|0|15||75.0 | nan | 27|55|86|20|48||140.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGAGACGCGCAAGGAGGAGGTGCTGACGGACTCACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRDAQGGGADGLTF | nan | :::::::::0:-1:15:::::20:-7:48::: |
| 29 | 4778 | 116 | 0.00173722 | TGTGCAATGATCGGGAACACAGGCTTTCAGAAACTTGTATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-3*00(277.1) | nan | TRAJ8*00(293.5) | TRAC*00(64.7) | 264|277|297|0|13|SG274T|51.0 | nan | 21|49|80|14|42||140.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAATGATCGGGAACACAGGCTTTCAGAAACTTGTATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAMIGNTGFQKLVF | nan | :::::::::0:0:13:::::14:-1:42::: |
| 30 | 4648 | 209 | 0.00168995 | TGTGCAGCAAGTATGTTCCCAGGAAGCCAAGGAAATCTCATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV13-1*00(291.4) | nan | TRAJ42*00(278.9) | TRAC*00(64.7) | 267|281|300|0|14||70.0 | nan | 30|55|86|20|45||125.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGCAAGTATGTTCCCAGGAAGCCAAGGAAATCTCATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAASMFPGSQGNLIF | nan | :::::::::0:1:14:::::20:-10:45::: |
| 31 | 4550 | 81 | 0.00165432 | TGTGTGGTGAACCCTAGGGACCAGTTCTATTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-1*00(303) | nan | TRAJ49*00(223.4) | TRAC*00(65.5) | 261|273|294|0|12||60.0 | nan | 31|45|76|19|33||70.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGTGGTGAACCCTAGGGACCAGTTCTATTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CVVNPRDQFYF | nan | :::::::::0:-1:12:::::19:-11:33::: |
| 32 | 4520 | 64 | 0.00164341 | TGCATCCTGGACGGCAAGCAGGGCGGATCTGAAAAGCTGGTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV26-2*00(267) | nan | TRAJ57*00(287.9) | TRAC*00(64.9) | 261|270|296|0|9||45.0 | nan | 25|52|83|18|45||135.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCATCCTGGACGGCAAGCAGGGCGGATCTGAAAAGCTGGTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CILDGKQGGSEKLVF | nan | :::::::::0:-6:9:::::18:-5:45::: |
| 33 | 4399 | 52 | 0.00159942 | TGTGCTGTGAGAGCGTATTTAGCAGGAAACACACCTCTTGTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV3*00(271.9) | nan | TRAJ29*00(270.3) | TRAC*00(64.5) | 270|283|306|0|13||65.0 | nan | 26|49|80|22|45||115.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGAGCGTATTTAGCAGGAAACACACCTCTTGTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRAYLAGNTPLVF | nan | :::::::::0:-3:13:::::22:-6:45::: |
| 34 | 4388 | 196 | 0.00159542 | TGTGCAGCAAGTTACCTCTATGGGAACAACAGACTCGCTTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV13-1*00(284.2) | nan | TRAJ7*00(278.3) | TRAC*00(64.7) | 267|283|300|0|15|DA279|63.0 | nan | 23|48|79|17|42||125.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGCAAGTTACCTCTATGGGAACAACAGACTCGCTTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAASYLYGNNRLAF | nan | :::::::::0:3:15:::::17:-3:42::: |
| 35 | 4359 | 37 | 0.00158487 | TGCATCGTCAGAGTCGCGGATCGGCAGTGCTTCCAAGATAATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV26-1*00(307.1) | nan | TRAJ3*00(271.1) | TRAC*00(64.8) | 261|279|297|0|18||90.0 | nan | 28|51|82|23|46||115.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCATCGTCAGAGTCGCGGATCGGCAGTGCTTCCAAGATAATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CIVRVADR_SASKIIF | nan | :::::::::0:2:18:::::23:-8:46::: |
| 36 | 4355 | 71 | 0.00158342 | TGTGCCGGGGGGGCGAATTATGGTGGTGCTACAAACAAGCTCATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(282.5) | nan | TRAJ32*00(323) | TRAC*00(64.7) | 264|271|297|0|7||35.0 | nan | 21|55|86|14|48||170.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGGGGGGGCGAATTATGGTGGTGCTACAAACAAGCTCATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAGGANYGGATNKLIF | nan | :::::::::0:-6:7:::::14:-1:48::: |
| 37 | 4320 | 34 | 0.00157069 | TGTGCAATGGAGGGGGATAGCAGCTATAAATTGATCTTC | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV14DV4*00(257.5) | nan | TRAJ12*00(278.6) | TRAC*00(70.5) | 273|290|310|0|16|DA282SA286G|54.0 | nan | 24|49|80|14|39||125.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAATGGAGGGGGATAGCAGCTATAAATTGATCTTC | 45 | nan | nan | nan | nan | nan | nan | nan | CAMEGDSSYKLIF | nan | :::::::::0:0:16:::::14:-4:39::: |
| 38 | 3833 | 39 | 0.00139363 | TGTGCTGTGAGACCCATTGATGGAGGAAGCCAAGGAAATCTCATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV3*00(268.2) | nan | TRAJ42*00(302.3) | TRAC*00(64.5) | 270|282|306|0|12||60.0 | nan | 23|55|86|15|48|I26G|148.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGACCCATTGATGGAGGAAGCCAAGGAAATCTCATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRPIDGGSQGNLIF | nan | :::::::::0:-4:12:::::15:-3:48::: |
| 39 | 3491 | 28 | 0.00126928 | TGCATCGTCAGAGTCTTATACTCTGGGGCTGGGAGTTACCAACTCACTTTC | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV26-1*00(297.7) | nan | TRAJ28*00(323) | TRAC*00(64.8) | 261|276|297|0|15||75.0 | nan | 11|55|86|8|51|SA17CSG19TDC20|175.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCATCGTCAGAGTCTTATACTCTGGGGCTGGGAGTTACCAACTCACTTTC | 45 | nan | nan | nan | nan | nan | nan | nan | CIVRVLYSGAGSYQLTF | nan | :::::::::0:-1:15:::::8:9:51::: |
| 40 | 3321 | 41 | 0.00120747 | TGTGCCGTCTTTTCGGGCACTGCCAGTAAACTCACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(282.3) | nan | TRAJ44*00(274.1) | TRAC*00(64.2) | 264|272|297|0|8||40.0 | nan | 28|52|83|15|39||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGTCTTTTCGGGCACTGCCAGTAAACTCACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVFSGTASKLTF | nan | :::::::::0:-5:8:::::15:-8:39::: |
| 41 | 3298 | 12 | 0.00119911 | TGCCTCGTGGGTGTTCTGGGGGTTACCAGAAAGTTACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV4*00(272.6) | nan | TRAJ13*00(292.8) | TRAC*00(73.1) | 261|274|297|0|13||65.0 | nan | 24|52|83|13|41||140.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCCTCGTGGGTGTTCTGGGGGTTACCAGAAAGTTACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CLVGVLG_YQKVTF | nan | :::::::::0:-3:13:::::13:-4:41::: |
| 42 | 3254 | 29 | 0.00118311 | TGTGCAATGAGAGAGAACACGGGCAGGAGAGCACTTACTTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV14DV4*00(276.6) | nan | TRAJ5*00(283.4) | TRAC*00(65.6) | 273|288|310|0|15||75.0 | nan | 23|49|80|16|42||130.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAATGAGAGAGAACACGGGCAGGAGAGCACTTACTTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAMRENTGRRALTF | nan | :::::::::0:-2:15:::::16:-3:42::: |
| 43 | 3099 | 83 | 0.00112676 | TGTGTGGTGAGCGACAGAGGCTCAACCCTGGGGAGGCTATACTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV10*00(274) | nan | TRAJ18*00(322.8) | TRAC*00(64.8) | 267|280|300|0|13||65.0 | nan | 21|55|86|11|45||170.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGTGGTGAGCGACAGAGGCTCAACCCTGGGGAGGCTATACTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CVVSDRGSTLGRLYF | nan | :::::::::0:0:13:::::11:-1:45::: |
| 44 | 2946 | 76 | 0.00107113 | TGTGCAGAGAATATTGCCCAGGCAGGAACTGCTCTGATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV13-2*00(301.4) | nan | TRAJ15*00(278.4) | TRAC*00(64.6) | 267|281|300|0|14||70.0 | nan | 24|49|80|17|42||125.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGAGAATATTGCCCAGGCAGGAACTGCTCTGATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAENIAQAGTALIF | nan | :::::::::0:1:14:::::17:-4:42::: |
| 45 | 2868 | 57 | 0.00104277 | TGTGCAGCAAGCCTTAGGACAGGAGGAAGCTACATACCTACATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV23DV6*00(269.4) | nan | TRAJ6*00(283.4) | TRAC*00(64.1) | 267|279|300|0|12||60.0 | nan | 25|51|82|19|45||130.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGCAAGCCTTAGGACAGGAGGAAGCTACATACCTACATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAASLRTGGSYIPTF | nan | :::::::::0:-1:12:::::19:-5:45::: |
| 46 | 2803 | 11 | 0.00101913 | TGCCTCGTGGGTGACATAGCAGCTATAAATTGATCTTC | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV4*00(290.4) | nan | TRAJ12*00(268.7) | TRAC*00(81.9) | 261|278|297|0|17||85.0 | nan | 26|49|80|15|38||115.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCCTCGTGGGTGACATAGCAGCTATAAATTGATCTTC | 45 | nan | nan | nan | nan | nan | nan | nan | CLVGDI_SYKLIF | nan | :::::::::0:1:17:::::15:-6:38::: |
| 47 | 2774 | 36 | 0.00100859 | TGTGCCGTGAATCGCTCTGACATGCGCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(299.9) | nan | TRAJ43*00(219) | TRAC*00(74) | 264|275|297|0|11||55.0 | nan | 30|43|74|17|30||65.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGTGAATCGCTCTGACATGCGCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVNRSDMRF | nan | :::::::::0:-2:11:::::17:-10:30::: |
| 48 | 2540 | 10 | 0.00092351 | TGCCTCGTGGGTCCTCTTTATAACCAGGGAGGAAAGCTTATCTTC | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV4*00(266.4) | nan | TRAJ23*00(298.1) | TRAC*00(66.3) | 261|273|297|0|12||60.0 | nan | 23|52|83|16|45||145.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCCTCGTGGGTCCTCTTTATAACCAGGGAGGAAAGCTTATCTTC | 45 | nan | nan | nan | nan | nan | nan | nan | CLVGPLYNQGGKLIF | nan | :::::::::0:-4:12:::::16:-3:45::: |
| 49 | 2526 | 24 | 0.00091842 | TGTGCTGTGAGAGACACCGCCCGGGTCGTGGAGGAGAGCACTTACTTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV3*00(288) | nan | TRAJ5*00(243.7) | TRAC*00(64.5) | 270|286|306|0|16||80.0 | nan | 31|49|80|31|49||90.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGAGACACCGCCCGGGTCGTGGAGGAGAGCACTTACTTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRDTAR_SWRRALTF | nan | :::::::::0:0:16:::::31:-11:49::: |
| 50 | 2499 | 12 | 0.000908603 | TGTGCCGTCCGAGGCTCCCGGAATAACAATGCCAGACTCATGTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV39*00(277.6) | nan | TRAJ31*00(303.8) | TRAC*00(62.4) | 264|272|297|0|8||40.0 | nan | 18|46|77|17|45||140.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGTCCGAGGCTCCCGGAATAACAATGCCAGACTCATGTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRGSRNNNARLMF | nan | :::::::::0:-5:8:::::17:2:45::: |
| 51 | 2475 | 9 | 0.000899877 | TGCCTCGTGGGTCCACTTTATAACCAGGGAGGAAAGCTTATCTTC | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV4*00(266.2) | nan | TRAJ23*00(299) | TRAC*00(66.4) | 261|273|297|0|12||60.0 | nan | 23|52|83|16|45||145.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCCTCGTGGGTCCACTTTATAACCAGGGAGGAAAGCTTATCTTC | 45 | nan | nan | nan | nan | nan | nan | nan | CLVGPLYNQGGKLIF | nan | :::::::::0:-4:12:::::16:-3:45::: |
| 52 | 2380 | 31 | 0.000865337 | TGTGCCGTGAATTCAGGATACAGCACCCTCACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(301.6) | nan | TRAJ11*00(292.4) | TRAC*00(64.7) | 264|275|297|0|11||55.0 | nan | 20|49|80|7|36||145.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGTGAATTCAGGATACAGCACCCTCACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVNSGYSTLTF | nan | :::::::::0:-2:11:::::7:0:36::: |
| 53 | 2335 | 46 | 0.000848975 | TGTGCTCTAGACGACGACTACAAGCTCAGCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV6*00(320.3) | nan | TRAJ20*00(252.4) | TRAC*00(65.1) | 267|279|300|0|12||60.0 | nan | 26|46|77|13|33||100.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTCTAGACGACGACTACAAGCTCAGCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CALDDDYKLSF | nan | :::::::::0:-1:12:::::13:-6:33::: |
| 54 | 2309 | 81 | 0.000839522 | TGTGCTTCTCCTGGGGCTGGGAGTTACCAACTCACTTTC | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV1-2*00(338.2) | nan | TRAJ28*00(298.1) | TRAC*00(64.7) | 261|267|295|0|6||30.0 | nan | 26|55|86|10|39||145.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTTCTCCTGGGGCTGGGAGTTACCAACTCACTTTC | 45 | nan | nan | nan | nan | nan | nan | nan | CASPGAGSYQLTF | nan | :::::::::0:-8:6:::::10:-6:39::: |
| 55 | 2237 | 69 | 0.000813344 | TGTGCTGTGAGATGGGCGGGAGGAAGCTACATACCTACATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV1-2*00(361.4) | nan | TRAJ6*00(272.7) | TRAC*00(64.6) | 261|273|295|0|12||60.0 | nan | 27|51|82|18|42||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGATGGGCGGGAGGAAGCTACATACCTACATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRWAGGSYIPTF | nan | :::::::::0:-2:12:::::18:-7:42::: |
| 56 | 2188 | 220 | 0.000795528 | TGTGCCGTGAGACGAGGTGGCAACACAGGCAAACTAATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-1*00(291.8) | nan | TRAJ37*00(278.2) | TRAC*00(64.6) | 270|280|304|0|10||50.0 | nan | 26|51|82|17|42||125.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGTGAGACGAGGTGGCAACACAGGCAAACTAATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRRGGNTGKLIF | nan | :::::::::0:-4:10:::::17:-6:42::: |
| 57 | 1983 | 40 | 0.000720993 | TGTGCTCTACGGGCGTACAGCAGTGCTTCCAAGATAATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV6*00(304) | nan | TRAJ3*00(301) | TRAC*00(64.8) | 267|276|300|0|9||45.0 | nan | 19|51|82|9|42|I23C|148.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTCTACGGGCGTACAGCAGTGCTTCCAAGATAATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CALRAYSSASKIIF | nan | :::::::::0:-4:9:::::9:1:42::: |
| 58 | 1961 | 20 | 0.000712994 | TGTGCTGTGTCCCAGGGGGATGGCCAGAAGCTGCTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-4*00(247.8) | nan | TRAJ16*00(258.8) | TRAC*00(78.5) | 270|279|304|0|9||45.0 | nan | 28|49|80|18|39||105.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGTCCCAGGGGGATGGCCAGAAGCTGCTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVSQGDGQKLLF | nan | :::::::::0:-5:9:::::18:-8:39::: |
| 59 | 1961 | 64 | 0.000712994 | TGTGCTGTGAGAGATAGCAACTATCAGTTAATCTGG | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV1-2*00(377.3) | nan | TRAJ33*00(272.5) | TRAC*00(64.7) | 261|276|295|0|15||75.0 | nan | 22|46|77|12|36||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGAGATAGCAACTATCAGTTAATCTGG | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRDSNYQLIW | nan | :::::::::0:1:15:::::12:-2:36::: |
| 60 | 1920 | 21 | 0.000698087 | TGTGCCCAGGGGACTGGAGGCTTCAAAACTATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(275.1) | nan | TRAJ9*00(272.8) | TRAC*00(64.7) | 264|270|297|0|6||30.0 | nan | 26|50|81|12|36||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCCAGGGGACTGGAGGCTTCAAAACTATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAQGTGGFKTIF | nan | :::::::::0:-7:6:::::12:-6:36::: |
| 61 | 1918 | 25 | 0.000697359 | TGTGCCGTGAAAAGGCCCACAGGCTTTCAGAAACTTGTATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(297.5) | nan | TRAJ8*00(278.9) | TRAC*00(64.5) | 264|275|297|0|11||55.0 | nan | 24|49|80|17|42||125.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGTGAAAAGGCCCACAGGCTTTCAGAAACTTGTATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVKRPTGFQKLVF | nan | :::::::::0:-2:11:::::17:-4:42::: |
| 62 | 1900 | 35 | 0.000690815 | GTATTTCCAAGGGGTTCAGGGAGCCCAGAAGCTGGTATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV27*00(225.3) | nan | TRAJ54*00(283.3) | TRAC*00(65.3) | 264|264|294|0|0||0.0 | nan | 23|49|80|14|40||130.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | GTATTTCCAAGGGGTTCAGGGAGCCCAGAAGCTGGTATTT | 45 | nan | nan | nan | nan | nan | nan | nan | VFPRGSG_AQKLVF | nan | :::::::::0:-10:0:::::14:-3:40::: |
| 63 | 1853 | 19 | 0.000673726 | TGTGCTGTGAGTGAAGGTGCAGGCAACATGCTCACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-4*00(270.8) | nan | TRAJ39*00(264.3) | TRAC*00(79) | 270|284|304|0|14||70.0 | nan | 30|52|83|17|39||110.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGTGAAGGTGCAGGCAACATGCTCACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVSEGAGNMLTF | nan | :::::::::0:0:14:::::17:-10:39::: |
| 64 | 1822 | 32 | 0.000662455 | TGTGCTCTGAGTGAAGAAGGTGGTACTAGCTATGGAAAGCTGACATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV9-2*00(248.4) | nan | TRAJ52*00(303.7) | TRAC*00(65.3) | 267|281|301|0|14||70.0 | nan | 28|58|89|18|48||150.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTCTGAGTGAAGAAGGTGGTACTAGCTATGGAAAGCTGACATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CALSEEGGTSYGKLTF | nan | :::::::::0:0:14:::::18:-8:48::: |
| 65 | 1783 | 16 | 0.000648275 | TGTGCTGTGAGAGACGGCGGGGGAAACAAACTGGTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV3*00(282) | nan | TRAJ47*00(243.6) | TRAC*00(77.1) | 270|285|306|0|15||75.0 | nan | 28|46|77|21|39||90.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGAGACGGCGGGGGAAACAAACTGGTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRDGGGNKLVF | nan | :::::::::0:-1:15:::::21:-8:39::: |
| 66 | 1748 | 51 | 0.00063555 | TGTGCAGAGACCGCCGTCAATACTGGAGGCTTCAAAACTATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV13-2*00(279.6) | nan | TRAJ9*00(288.4) | TRAC*00(64.7) | 267|277|300|0|10||50.0 | nan | 23|50|81|18|45||135.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGAGACCGCCGTCAATACTGGAGGCTTCAAAACTATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAETAVNTGGFKTIF | nan | :::::::::0:-3:10:::::18:-3:45::: |
| 67 | 1742 | 23 | 0.000633368 | TGTGTTGTGAGTGAATGGCAGGCAGGAACTGCTCTGATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-2*00(274.9) | nan | TRAJ15*00(272.6) | TRAC*00(69.8) | 270|284|304|0|14||70.0 | nan | 25|49|80|18|42||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGTTGTGAGTGAATGGCAGGCAGGAACTGCTCTGATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CVVSEWQAGTALIF | nan | :::::::::0:0:14:::::18:-5:42::: |
| 68 | 1673 | 15 | 0.000608281 | TGTGCAATGAGAGAGGGCGGATTCACGGGAGGAGGAAACAAACTCACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV14DV4*00(296.2) | nan | TRAJ10*00(297.1) | TRAC*00(64.5) | 273|291|310|0|18||90.0 | nan | 24|53|84|22|51||145.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAATGAGAGAGGGCGGATTCACGGGAGGAGGAAACAAACTCACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAMREGGFTGGGNKLTF | nan | :::::::::0:1:18:::::22:-4:51::: |
| 69 | 1610 | 22 | 0.000585375 | TGCATCCTGAGAGACCGGGGCGGGGCAAACAACCTCTTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV26-2*00(296.7) | nan | TRAJ36*00(257.9) | TRAC*00(64.8) | 261|276|296|0|15||75.0 | nan | 27|48|79|21|42||105.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCATCCTGAGAGACCGGGGCGGGGCAAACAACCTCTTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CILRDRGGANNLFF | nan | :::::::::0:0:15:::::21:-7:42::: |
| 70 | 1557 | 101 | 0.000566105 | TGTGCTCTGAGTGAGGAGAAGAGGGATAGCAGCTATAAATTGATCTTC | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV19*00(297.2) | nan | TRAJ12*00(279.6) | TRAC*00(64.8) | 273|289|310|0|16||80.0 | nan | 21|49|80|20|48|ST23G|126.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTCTGAGTGAGGAGAAGAGGGATAGCAGCTATAAATTGATCTTC | 45 | nan | nan | nan | nan | nan | nan | nan | CALSEEKRDSSYKLIF | nan | :::::::::0:-1:16:::::20:-1:48::: |
| 71 | 1535 | 110 | 0.000558106 | TGTGCTCTGAGTGAGGCGTGGGGAGCCCAGAAGCTGGTATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV19*00(309.2) | nan | TRAJ54*00(263.4) | TRAC*00(64.9) | 273|291|310|0|18||90.0 | nan | 27|49|80|20|42||110.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTCTGAGTGAGGCGTGGGGAGCCCAGAAGCTGGTATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CALSEAWGAQKLVF | nan | :::::::::0:1:18:::::20:-7:42::: |
| 72 | 1535 | 9 | 0.000558106 | TGCATCGTCAGACCTCAGGAATATGGAAACAAACTGGTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV26-1*00(278.1) | nan | TRAJ47*00(278) | TRAC*00(64.8) | 261|273|297|0|12||60.0 | nan | 21|46|77|17|42||125.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCATCGTCAGACCTCAGGAATATGGAAACAAACTGGTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CIVRPQEYGNKLVF | nan | :::::::::0:-4:12:::::17:-1:42::: |
| 73 | 1500 | 23 | 0.00054538 | TGTGCCGTGAACAATCCAAACTATGGTCAGAATTTTGTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(307.5) | nan | TRAJ26*00(272.5) | TRAC*00(64.6) | 264|277|297|0|13||65.0 | nan | 25|49|80|18|42||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGTGAACAATCCAAACTATGGTCAGAATTTTGTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVNNPNYGQNFVF | nan | :::::::::0:0:13:::::18:-5:42::: |
| 74 | 1494 | 8 | 0.000543199 | TGCCTCTGCGAGGGAGCAGGCAAATCAACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV4*00(243.4) | nan | TRAJ27*00(246.2) | TRAC*00(104.2) | 261|267|297|0|6||30.0 | nan | 30|48|79|15|33||90.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCCTCTGCGAGGGAGCAGGCAAATCAACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CLCEGAGKSTF | nan | :::::::::0:-10:6:::::15:-10:33::: |
| 75 | 1458 | 46 | 0.00053011 | TGCGCTGTGAGGCGGAGCTGGGGGAAATTGCAGTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV1-1*00(358.3) | nan | TRAJ24*00(258) | TRAC*00(64.9) | 261|272|295|0|11||55.0 | nan | 31|52|83|15|36||105.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCGCTGTGAGGCGGAGCTGGGGGAAATTGCAGTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRRSWGKLQF | nan | :::::::::0:-3:11:::::15:-11:36::: |
| 76 | 1448 | 43 | 0.000526474 | TGTGCTGCCATGGATAGCAACTATCAGTTAATCTGG | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV1-2*00(343.2) | nan | TRAJ33*00(297.7) | TRAC*00(64.8) | 261|268|295|0|7||35.0 | nan | 17|46|77|7|36||145.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGCCATGGATAGCAACTATCAGTTAATCTGG | 45 | nan | nan | nan | nan | nan | nan | nan | CAAMDSNYQLIW | nan | :::::::::0:-7:7:::::7:3:36::: |
| 77 | 1446 | 7 | 0.000525746 | TGCCTCGTGGGTGGAGGATTCATGGAATATGGAAACAAACTGGTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV4*00(270.4) | nan | TRAJ47*00(296.6) | TRAC*00(64.5) | 261|274|297|0|13||65.0 | nan | 14|46|77|17|48|DC18|143.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCCTCGTGGGTGGAGGATTCATGGAATATGGAAACAAACTGGTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CLVGGGFMEYGNKLVF | nan | :::::::::0:-3:13:::::17:6:48::: |
| 78 | 1436 | 10 | 0.000522111 | TGCATCGTCAGACGACTGTCTAACGACTACAAGCTCAGCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV26-1*00(278) | nan | TRAJ20*00(273.7) | TRAC*00(65.1) | 261|273|297|0|12||60.0 | nan | 22|46|77|18|42||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCATCGTCAGACGACTGTCTAACGACTACAAGCTCAGCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CIVRRLSNDYKLSF | nan | :::::::::0:-4:12:::::18:-2:42::: |
| 79 | 1435 | 18 | 0.000521747 | TGTGCTGTGAGTTCCTCAGGGACACAGGCTTTCAGAAACTTGTATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-4*00(263.6) | nan | TRAJ8*00(285.4) | TRAC*00(64.5) | 270|282|304|0|12||60.0 | nan | 17|49|80|15|47|ST20GSA22G|132.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGTTCCTCAGGGACACAGGCTTTCAGAAACTTGTATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVSSSGT_GFQKLVF | nan | :::::::::0:-2:12:::::15:3:47::: |
| 80 | 1434 | 19 | 0.000521383 | TGTGCCTTTTCAGATGGCCAGAAGCTGCTCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV24*00(258.9) | nan | TRAJ16*00(287.7) | TRAC*00(95.4) | 267|276|297|0|9||45.0 | nan | 22|49|80|6|33||135.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCTTTTCAGATGGCCAGAAGCTGCTCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAFSDGQKLLF | nan | :::::::::0:-1:9:::::6:-2:33::: |
| 81 | 1382 | 15 | 0.000502477 | TGTGCTGTGAGAGACATGGGGCCAACGGGCAGGAGAGCACTTACTTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV3*00(297.2) | nan | TRAJ5*00(273.7) | TRAC*00(64.8) | 270|288|306|0|18||90.0 | nan | 25|49|80|24|48||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGAGAGACATGGGGCCAACGGGCAGGAGAGCACTTACTTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVRDMGPTGRRALTF | nan | :::::::::0:2:18:::::24:-5:48::: |
| 82 | 1361 | 15 | 0.000494842 | TGTGTTGTGACTCAGGGAACTGGAGGCTTCAAAACTATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-2*00(251.6) | nan | TRAJ9*00(272.9) | TRAC*00(69) | 270|280|304|0|10||50.0 | nan | 26|50|81|18|42||120.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGTTGTGACTCAGGGAACTGGAGGCTTCAAAACTATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CVVTQGTGGFKTIF | nan | :::::::::0:-4:10:::::18:-6:42::: |
| 83 | 1340 | 101 | 0.000487206 | TGTGCAGAGGGTTTTCTAACGACTACAAGCTCAGCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV5*00(277.3) | nan | TRAJ20*00(279.2) | TRAC*00(64.8) | 264|276|297|0|12|SA273G|46.0 | nan | 21|46|77|13|38||125.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGAGGGTTTTCTAACGACTACAAGCTCAGCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAEGFL_DYKLSF | nan | :::::::::0:-1:12:::::13:-1:38::: |
| 84 | 1329 | 4 | 0.000483207 | TGCCTAATAAAGGAAATGGGAGCCCAGAAGCTGGTATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV40*00(242.2) | nan | TRAJ54*00(262.7) | TRAC*00(65) | 249|254|283|0|5|ST251C|11.0 | nan | 27|49|80|17|39||110.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCCTAATAAAGGAAATGGGAGCCCAGAAGCTGGTATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CLIKEMGAQKLVF | nan | :::::::::0:-9:5:::::17:-7:39::: |
| 85 | 1316 | 37 | 0.00047848 | TGTGCTGTGGGTGCTCATGGAGGAAGCCAAGGAAATCTCATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV8-3*00(273.4) | nan | TRAJ42*00(298.7) | TRAC*00(64.8) | 270|287|304|0|17|SG284T|71.0 | nan | 26|55|86|16|45||145.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGGGTGCTCATGGAGGAAGCCAAGGAAATCTCATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVGAHGGSQGNLIF | nan | :::::::::0:3:17:::::16:-6:45::: |
| 86 | 1304 | 41 | 0.000474117 | TGTGCTGTGATGGATAGCAACTATCAGTTAATCTGG | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV1-2*00(355.9) | nan | TRAJ33*00(287.3) | TRAC*00(64.6) | 261|271|295|0|10||50.0 | nan | 19|46|77|9|36||135.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGATGGATAGCAACTATCAGTTAATCTGG | 45 | nan | nan | nan | nan | nan | nan | nan | CAVMDSNYQLIW | nan | :::::::::0:-4:10:::::9:1:36::: |
| 87 | 1300 | 7 | 0.000472663 | TGCCTCGTGGTCCCCTCCGAGCGGAGAAAGCTTATCTTC | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV4*00(259.5) | nan | TRAJ23*00(226.4) | TRAC*00(78.3) | 261|271|297|0|10||50.0 | nan | 34|52|83|22|39|DG38|73.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCCTCGTGGTCCCCTCCGAGCGGAGAAAGCTTATCTTC | 45 | nan | nan | nan | nan | nan | nan | nan | CLVVPSERRKLIF | nan | :::::::::0:-6:10:::::22:-14:39::: |
| 88 | 1294 | 37 | 0.000470481 | TGCGCTGTGAGTCGGGATAGCAGCTATAAATTGATCTTC | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV1-1*00(356.3) | nan | TRAJ12*00(278) | TRAC*00(64.6) | 261|272|295|0|11||55.0 | nan | 24|49|80|14|39||125.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCGCTGTGAGTCGGGATAGCAGCTATAAATTGATCTTC | 45 | nan | nan | nan | nan | nan | nan | nan | CAVSRDSSYKLIF | nan | :::::::::0:-3:11:::::14:-4:39::: |
| 89 | 1285 | 54 | 0.000467209 | TGTGCTGTGGTGGCTCTAGCAACACAGGCAAACTAATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV2*00(272.8) | nan | TRAJ37*00(279.2) | TRAC*00(65) | 249|265|283|0|16|SA259TSA262C|52.0 | nan | 20|51|82|10|41|SG27A|141.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCTGTGGTGGCTCTAGCAACACAGGCAAACTAATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVVALA_TGKLIF | nan | :::::::::0:2:16:::::10:0:41::: |
| 90 | 1284 | 19 | 0.000466845 | TGTGTGGTGAACCCCACCGACAAGCTCATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-1*00(303.8) | nan | TRAJ34*00(248.4) | TRAC*00(65.5) | 261|273|294|0|12||60.0 | nan | 28|47|78|14|33||95.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGTGGTGAACCCCACCGACAAGCTCATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CVVNPTDKLIF | nan | :::::::::0:-1:12:::::14:-8:33::: |
| 91 | 1276 | 4 | 0.000463937 | TGCCTCGTGGTCAAGGGGGGAAGCCAAGGAAATCTCATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV4*00(258.3) | nan | TRAJ42*00(274.2) | TRAC*00(71.5) | 261|271|297|0|10||50.0 | nan | 28|55|86|15|42|SA30G|121.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCCTCGTGGTCAAGGGGGGAAGCCAAGGAAATCTCATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CLVVKGGSQGNLIF | nan | :::::::::0:-6:10:::::15:-8:42::: |
| 92 | 1268 | 9 | 0.000461028 | TGTGCAATGAGGCCGAATTCAGGATACAGCACCCTCACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV14DV4*00(256.1) | nan | TRAJ11*00(292.8) | TRAC*00(65.1) | 273|284|310|0|11||55.0 | nan | 21|49|80|14|42||140.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAATGAGGCCGAATTCAGGATACAGCACCCTCACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAMRPNSGYSTLTF | nan | :::::::::0:-6:11:::::14:-1:42::: |
| 93 | 1260 | 10 | 0.000458119 | TGTGCAACGTTCGAATTCAGGATACAGCACCCTCACCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV14DV4*00(239.4) | nan | TRAJ11*00(292.8) | TRAC*00(63.8) | 273|280|310|0|7||35.0 | nan | 21|49|80|12|40||140.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAACGTTCGAATTCAGGATACAGCACCCTCACCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CATFEFR_YSTLTF | nan | :::::::::0:-10:7:::::12:-1:40::: |
| 94 | 1250 | 19 | 0.000454483 | TGTGCCGTGAAAGGGGGGAACAACAGACTCGCTTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV12-2*00(294.9) | nan | TRAJ7*00(258.7) | TRAC*00(64.5) | 264|275|297|0|11||55.0 | nan | 27|48|79|15|36||105.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCCGTGAAAGGGGGGAACAACAGACTCGCTTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAVKGGNNRLAF | nan | :::::::::0:-2:11:::::15:-7:36::: |
| 95 | 1233 | 4 | 0.000448303 | TGTCTTCTGGGAGATTTCACTGGAGGTAGCAACTATAAACTGACATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV40*00(304) | nan | TRAJ53*00(293.4) | TRAC*00(64.7) | 249|267|283|0|18|SC264T|76.0 | nan | 27|55|86|20|48||140.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTCTTCTGGGAGATTTCACTGGAGGTAGCAACTATAAACTGACATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CLLGDFTGGSNYKLTF | nan | :::::::::0:4:18:::::20:-7:48::: |
| 96 | 1230 | 7 | 0.000447212 | TGCATCGTCAGAGCACGGAATTATGGAGGAAGCCAAGGAAATCTCATCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV26-1*00(289) | nan | TRAJ42*00(322.6) | TRAC*00(64.8) | 261|274|297|0|13||65.0 | nan | 21|55|86|17|51||170.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCATCGTCAGAGCACGGAATTATGGAGGAAGCCAAGGAAATCTCATCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CIVRARNYGGSQGNLIF | nan | :::::::::0:-3:13:::::17:-1:51::: |
| 97 | 1199 | 7 | 0.000435941 | TGCATCGTCAGAGTGGGGGACATGCGCTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV26-1*00(293.1) | nan | TRAJ43*00(213.9) | TRAC*00(107.1) | 261|275|297|0|14||70.0 | nan | 31|43|74|18|30||60.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGCATCGTCAGAGTGGGGGACATGCGCTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CIVRVGDMRF | nan | :::::::::0:-2:14:::::18:-11:30::: |
| 98 | 1182 | 17 | 0.00042976 | TGTGCAGGAGTAGGGGGAGGTAGCAACTATAAACTGACATTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV27*00(266.9) | nan | TRAJ53*00(288.4) | TRAC*00(64.8) | 264|274|294|0|10||50.0 | nan | 28|55|86|15|42||135.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAGGAGTAGGGGGAGGTAGCAACTATAAACTGACATTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAGVGGGSNYKLTF | nan | :::::::::0:0:10:::::15:-8:42::: |
| 99 | 1168 | 12 | 0.000424669 | TGTGCAATGAGCTGGTTTTCTGGTGGCTACAATAAGCTGATTTTT | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | TRAV14DV4*00(257.5) | nan | TRAJ4*00(307.7) | TRAC*00(65.1) | 273|284|310|0|11||55.0 | nan | 21|52|83|14|45||155.0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | TGTGCAATGAGCTGGTTTTCTGGTGGCTACAATAAGCTGATTTTT | 45 | nan | nan | nan | nan | nan | nan | nan | CAMSWFSGGYNKLIF | nan | :::::::::0:-6:11:::::14:-1:45::: |
In order to run the analysis for all samples in the project on Linux we can use GNU Parallel in the following way:
#!/usr/bin/env bash
mkdir -p results
ls /raw/*R1* |
parallel -j 2 --line-buffer \
"mixcr analyze miltenyi-human-rna-tcr-profiling \
{} \
{=s:R1:R2:=} \
{=s:.*/:results/:;s:_R.*::=}"
Under the hood pipeline
Under the hood miltenyi-human-rna-tcr-profiling preset actually executes the following pipeline:
align
Alignment of raw sequencing reads against reference database of V-, D-, J- and C- gene segments.
mixcr align \
--species hsa \
-p generic-amplicon-with-umi \
-OvParameters.geneFeatureToAlign="VTranscriptWithout5UTRWithP" \
-OvParameters.parameters.floatingLeftBound=false \
-OjParameters.parameters.floatingRightBound=false \
-OсParameters.parameters.floatingRightBound=false \
--tag-pattern "^N{0:2}tggtatcaacgcagagt(UMI:N{14})N{21}(R1:*) \ ^N{20}(R2:*)" \
--report results/Multi_TRA_FS115_1.report.txt \
--json-report results/Multi_TRA_FS115_1.report.json \
raw/Multi_TRA_FS115_1_R1.fastq.gz \
raw/Multi_TRA_FS115_1_R2.fastq.gz \
results/Multi_TRA_FS115_1.vdjca
Option --report is specified here explicitly.
--species hsa- determines the organism species (hsa for Homo Sapiens).
-p generic-amplicon- a generic preset of MiXCR parameters for amplicon data.
-OvParameters.geneFeatureToAlign="VTranscriptWithout5UTRWithP"- Sets a V gene feature to align. Check gene features for more info.
-OvParameters.parameters.floatingLeftBound=false- Results in a global alignment algorithm for V gene left bound. We use it because primer sequences were trimmed with
--tagPattern. -OjParameters.parameters.floatingRightBound=false- Results in a global alignment algorithm for J gene right bound due to the absence of primer sequences.
-OcParameters.parameters.floatingRightBound=false- Results in a local alignment algorithm for C gene right bound.We use it because primer sequences were trimmed with
--tagPattern. --tagPattern "^N{0:2}tggtatcaacgcagagt(UMI:N{14})N{21}(R1:*) \ ^N{20}(R2:*)"- tag pattern specifies the location of the UMI barcode according to the library structure and trims primers sequences.
refineTagsAndSort
Corrects sequencing and PCR errors inside barcode sequences. This step does extremely important job by correcting artificial diversity caused by errors in barcodes. In the considered example project it corrects only sequences of UMIs.
mixcr refineTagsAndSort \
--report results/Multi_TRA_FS115_1.report.txt \
--json-report results/Multi_TRA_FS115_1.report.json \
results/Multi_TRA_FS115_1.vdjca \
results/Multi_TRA_FS115_1.refined.vdjca
assemble
Assembles clonotypes and applies several layers of errors correction:
- quality-dependent correction for sequencing errors
- PCR-error correction by clustering
- UMI-based error correction)
Check mixcr assemble for more information.
mixcr assemble \
-OassemblingFeatures="CDR3"
-OseparateByJ=true \
-OseparateByV=true \
--report results/Multi_TRA_FS115_1.report.txt \
--json-report results/Multi_TRA_FS115_1.report.json \
results/Multi_TRA_FS115_1.refined.vdjca \
results/Multi_TRA_FS115_1.clns
Options --report and --json-report are specified here explicitly so that the report files will be appended with assembly report.
-OassemblingFeatures=CDR3- By default
qiaseq-human-tcr-cdr3preset assembles clones byCDR3sequence. -separateByJ: true- Separate clones with the same assembling feature, but different V-genes.
-separateByV: true- Separate clones with the same assembling feature, but different J-genes.
export
Exports clonotypes from .clns file into human-readable tables.
mixcr exportClones \
-c TRA \
-uniqueTagCount UMI \
results/Multi_TRA_FS115_1.clns \
results/Multi_TRA_FS115_1.clones.TRA.txt
-с TRA- defines a specific chain to be exported.
-uniqueTagCount UMI- adds a column with the number of UMIs for each clone.
Quality control
Now when we have all files processed lets perform Quality Control. That can be easily done using mixcr exportQc function.
mixcr exportQc align results/*.clns figs/alignQc.pdf
From this plot we can tell that all samples have high alignment rate, more than 90% of reads have been successfully aligned to the reference sequences and CDR3 has been established.
Now we can check chain distribution plot:
mixcr exportQc chainUsage results/*.clns figs/chainUsage.pdf
Here we can see that no cross-contamination has occurred. TCR alpha samples consist only of TRA clones, and TCR betta only of TRB.
Reports
Finally, MiXCR provides a very convenient way to look at the reports generated at ech step. Every .vdjca, .clns and .clna file holds all the reports for every MiXCR function that has been applied to this sample. E.g. in our case .clns file contains reports for mixcr align and mixcr assemble. To output this report use mixcr exportReports as shown bellow. Note --json parameter will output a JSON-formatted report.
mixcr exportReports \
results/Multi_TRA_FS115_1.clns \
results/Multi_TRA_FS115_1.report.txt
mixcr exportReports \
--json \
results/Multi_TRA_FS115_1.clns \
results/Multi_TRA_FS115_1.report.json
Show report file
============== Align Report ==============
============== Align Report ==============
Total sequencing reads: 3567679
Successfully aligned reads: 3448515 (96.66%)
Chimeras: 4 (0%)
Paired-end alignment conflicts eliminated: 80984 (2.27%)
Alignment failed, no hits (not TCR/IG?): 2855 (0.08%)
Alignment failed because of absence of V hits: 24752 (0.69%)
Alignment failed because of absence of J hits: 62293 (1.75%)
No target with both V and J alignments: 11677 (0.33%)
Alignment failed because of low total score: 157 (0%)
Absent barcode: 17430 (0.49%)
Overlapped: 3272356 (91.72%)
Overlapped and aligned: 3218859 (90.22%)
Alignment-aided overlaps: 3992 (0.12%)
Overlapped and not aligned: 53497 (1.5%)
No CDR3 parts alignments, percent of successfully aligned: 1211 (0.04%)
Partial aligned reads, percent of successfully aligned: 34409 (1%)
V gene chimeras: 57 (0%)
J gene chimeras: 2004 (0.06%)
TRA chains: 3448272 (99.99%)
TRA non-functional: 355157 (10.3%)
TRB chains: 111 (0%)
TRB non-functional: 20 (18.02%)
TRD chains: 128 (0%)
TRD non-functional: 31 (24.22%)
Realigned with forced non-floating bound: 563770 (15.8%)
Realigned with forced non-floating right bound in left read: 43576 (1.22%)
Realigned with forced non-floating left bound in right read: 43576 (1.22%)
Tag parsing report:
Total reads: 3567679
Matched reads: 3550249 (99.51%)
Projection +R1 +R2: 3550249 (99.51%)
For variant 0:
For projection [1, 2]:
UMI:Left position:
17: + 982994 (27.69%) = 982994 (27.69%)
18: + 1232085 (34.7%) = 2215079 (62.39%)
19: + 1335170 (37.61%) = 3550249 (100%)
UMI:Right position:
31: + 982994 (27.69%) = 982994 (27.69%)
32: + 1232085 (34.7%) = 2215079 (62.39%)
33: + 1335170 (37.61%) = 3550249 (100%)
R1:Left position:
52: + 982994 (27.69%) = 982994 (27.69%)
53: + 1232085 (34.7%) = 2215079 (62.39%)
54: + 1335170 (37.61%) = 3550249 (100%)
R1:Right position:
52~146: + 255675 (7.2%) = 255675 (7.2%)
147: + 659338 (18.57%) = 915013 (25.77%)
148: + 1760294 (49.58%) = 2675307 (75.36%)
149: + 874942 (24.64%) = 3550249 (100%)
R2:Left position: 20
Variants: 0
Cost:
0: + 3433842 (96.72%) = 3433842 (96.72%)
5~10: + 116407 (3.28%) = 3550249 (100%)
UMI length: 14
R1 length:
0~93: + 179299 (5.05%) = 179299 (5.05%)
94: + 1523494 (42.91%) = 1702793 (47.96%)
95: + 951209 (26.79%) = 2654002 (74.76%)
96~97: + 896247 (25.24%) = 3550249 (100%)
R2 length:
15~127: + 291090 (8.2%) = 291090 (8.2%)
128: + 1098902 (30.95%) = 1389992 (39.15%)
129: + 2160257 (60.85%) = 3550249 (100%)
============== RefineTagsAndSort Report ==============
============== RefineTagsAndSort Report ==============
Time spent in correction: 0ns
UMI input diversity: 266703
UMI output diversity: 137060 (51.39%)
UMI input reads: 3448498
UMI output count: 3448497 (100%)
UMI mean reads per tag: 12.93
UMI input core diversity: 266674 (99.99%)
UMI input core reads: 3448469 (100%)
UMI directly corrected diversity: 129642 (48.61%)
UMI directly corrected reads: 144398 (4.19%)
UMI diversity filtered by tag quality: 1 (0%)
UMI reads filtered by tag quality: 1 (0%)
UMI diversity filtered by whitelist: 0 (0%)
UMI recursively corrected: 6799
Number of output records: 3302573 (95.77%)
Filter report:
Number of groups: 137060
Number of groups accepted: 53937 (39.35%)
Total records weight: 3448497.0
Records weight accepted: 3302573.0 (95.77%)
Operator #0:
Effective threshold: 8.0
============== Assemble Report ==============
============== Assemble Report ==============
Number of input groups: 53937
Number of input alignments: 3302573
Number of output pre-clonotypes: 50730
Number of clonotypes per group:
0: + 3239 (6.01%) = 3239 (6.01%)
1: + 50558 (93.83%) = 53797 (99.84%)
2: + 86 (0.16%) = 53883 (100%)
Number of core alignments: 2748073 (83.21%)
Discarded core alignments: 504431 (18.36%)
Empirically assigned alignments: 8264 (0.25%)
Empirical assignment conflicts: 0 (0%)
UMI+VJ-gene empirically assigned alignments: 8264 (0.25%)
VJ-gene empirically assigned alignments: 0 (0%)
UMI empirically assigned alignments: 0 (0%)
Number of ambiguous UMIs: 86
Number of ambiguous V-genes: 3
Number of ambiguous J-genes: 1
Number of ambiguous UMI+V/J-gene combinations: 4
Unassigned alignments: 545221 (16.51%)
Final clonotype count: 27957
Average number of reads per clonotype: 98.38
Reads used in clonotypes, percent of total: 2750375 (77.09%)
Reads used in clonotypes before clustering, percent of total: 2755131 (77.22%)
Number of reads used as a core, percent of used: 2755073 (100%)
Mapped low quality reads, percent of used: 58 (0%)
Reads clustered in PCR error correction, percent of used: 4756 (0.17%)
Reads pre-clustered due to the similar VJC-lists, percent of used: 30 (0%)
Reads dropped due to the lack of a clone sequence, percent of total: 50069 (1.4%)
Reads dropped due to a too short clonal sequence, percent of total: 52 (0%)
Reads dropped due to low quality, percent of total: 0 (0%)
Reads dropped due to failed mapping, percent of total: 1154 (0.03%)
Reads dropped with low quality clones, percent of total: 0 (0%)
Clonotypes eliminated by PCR error correction: 88
Clonotypes dropped as low quality: 0
Clonotypes pre-clustered due to the similar VJC-lists: 1
TRA chains: 27956 (100%)
TRA non-functional: 2833 (10.13%)
TRD chains: 1 (0%)
TRD non-functional: 1 (100%)
{
"align": {
"type": "alignerReport",
"commandLine": "--report results/Multi_TRA_FS115_1.align.report.txt --json-report results/Multi_TRA_FS115_1.align.report.json --preset milab-human-tcr-rna-multiplex-cdr3 /raw/2s3/milab-tcr-mulriplex/Multi_TRA_FS115_1_S149_R1_001.fastq.gz /raw/2s3/milab-tcr-mulriplex/Multi_TRA_FS115_1_S149_R2_001.fastq.gz results/Multi_TRA_FS115_1.vdjca",
"inputFiles": [
"/raw/2s3/milab-tcr-mulriplex/Multi_TRA_FS115_1_S149_R1_001.fastq.gz",
"/raw/2s3/milab-tcr-mulriplex/Multi_TRA_FS115_1_S149_R2_001.fastq.gz"
],
"outputFiles": [
"results/Multi_TRA_FS115_1.vdjca"
],
"version": "4.0.0-432-protocols; built=Tue Oct 11 09:48:35 CEST 2022; rev=2b3b93fc41; lib=repseqio.v2.0",
"trimmingReport": null,
"totalReadsProcessed": 3567679,
"aligned": 3448515,
"notAligned": 119164,
"notAlignedReasons": {
"LowTotalScore": 157,
"NoVHits": 24752,
"NoJHits": 62293,
"NoBarcode": 17430,
"NoCDR3Parts": 0,
"VAndJOnDifferentTargets": 11677,
"NoHits": 2855
},
"chimeras": 4,
"overlapped": 3272356,
"alignmentAidedOverlaps": 3992,
"overlappedAligned": 3218859,
"overlappedNotAligned": 53497,
"pairedEndAlignmentConflicts": 80984,
"vChimeras": 57,
"jChimeras": 2004,
"chainUsage": {
"type": "chainUsage",
"chimeras": 4,
"total": 3448515,
"chains": {
"TRA": {
"total": 3448272,
"nonFunctional": 355157,
"isOOF": 319826,
"hasStops": 35331
},
"TRB": {
"total": 111,
"nonFunctional": 20,
"isOOF": 6,
"hasStops": 14
},
"TRD": {
"total": 128,
"nonFunctional": 31,
"isOOF": 30,
"hasStops": 1
}
}
},
"realignedWithForcedNonFloatingBound": 563770,
"realignedWithForcedNonFloatingRightBoundInLeftRead": 43576,
"realignedWithForcedNonFloatingLeftBoundInRightRead": 43576,
"noCDR3PartsAlignments": 1211,
"partialAlignments": 34409,
"tagParsingReport": {
"total": 3567679,
"matched": 3550249,
"totalBitCost": 595287.5547334387,
"projections": {
"1,2": 3550249
},
"detailedReport": [
{
"nested": {
"1,2": {
"variantId": 0,
"nested": [
[
{
"positionDistributions": {
"UMI:Left": {
"17": 982994,
"18": 1232085,
"19": 1335170
},
"UMI:Right": {
"32": 1232085,
"33": 1335170,
"31": 982994
},
"R1:Left": {
"52": 982994,
"53": 1232085,
"54": 1335170
},
"R1:Right": {
"128": 199,
"129": 217,
"130": 56,
"131": 45,
"132": 304,
"133": 556,
"134": 1335,
"135": 1162,
"136": 1327,
"137": 493,
"138": 640,
"139": 668,
"140": 639,
"141": 1721,
"142": 2101,
"143": 2310,
"144": 1097,
"145": 17799,
"146": 200055,
"147": 659338,
"148": 1760294,
"149": 874942,
"52": 1,
"53": 1,
"54": 4,
"55": 13,
"56": 18,
"58": 13,
"59": 12,
"60": 12,
"66": 5,
"67": 11,
"68": 31,
"69": 31,
"70": 1,
"71": 5,
"72": 6,
"73": 39,
"74": 451,
"75": 685,
"76": 811,
"77": 200,
"78": 11,
"79": 37,
"80": 64,
"81": 45,
"82": 8,
"83": 13,
"84": 27,
"85": 26,
"86": 142,
"87": 185,
"88": 177,
"89": 26,
"90": 26,
"91": 50,
"92": 152,
"93": 222,
"94": 248,
"95": 26,
"96": 4,
"97": 28,
"98": 239,
"99": 1421,
"100": 2175,
"101": 5016,
"102": 4388,
"103": 4156,
"104": 127,
"105": 22,
"106": 37,
"107": 38,
"108": 36,
"109": 20,
"110": 1,
"111": 5,
"113": 1,
"114": 32,
"115": 27,
"116": 35,
"117": 8,
"118": 15,
"119": 224,
"120": 266,
"121": 266,
"122": 35,
"123": 29,
"124": 114,
"125": 104,
"126": 121,
"127": 126
}
},
"lengthDistributions": {
"UMI": {
"14": 3550249
},
"R1": {
"0": 1,
"1": 1,
"2": 32,
"3": 1,
"4": 4,
"5": 4,
"6": 31,
"14": 11,
"15": 66,
"16": 1,
"17": 1,
"18": 2,
"19": 10,
"20": 8,
"21": 119,
"22": 1522,
"23": 528,
"24": 3,
"25": 17,
"26": 34,
"27": 110,
"29": 1,
"30": 44,
"31": 1,
"32": 8,
"33": 65,
"34": 453,
"35": 7,
"36": 9,
"37": 78,
"38": 8,
"39": 36,
"40": 558,
"41": 59,
"42": 2,
"43": 3,
"44": 17,
"45": 87,
"46": 658,
"47": 4287,
"48": 1740,
"49": 10472,
"50": 265,
"51": 28,
"52": 29,
"53": 17,
"54": 58,
"55": 46,
"57": 5,
"58": 1,
"59": 1,
"61": 1,
"62": 86,
"63": 12,
"64": 3,
"65": 6,
"66": 47,
"67": 714,
"68": 10,
"69": 5,
"70": 81,
"71": 19,
"72": 273,
"73": 11,
"74": 60,
"75": 373,
"76": 164,
"77": 14,
"78": 21,
"79": 91,
"80": 1196,
"81": 187,
"82": 2947,
"83": 194,
"84": 543,
"85": 939,
"86": 292,
"87": 719,
"88": 984,
"89": 4240,
"90": 1525,
"91": 14789,
"92": 33248,
"93": 93956,
"94": 1523494,
"95": 951209,
"96": 509864,
"97": 386383
}
},
"costDistributions": {
"0": 3433842,
"5": 109648,
"10": 6759
},
"variantDistribution": {
"0": 3550249
}
}
],
[
{
"positionDistributions": {
"R2:Left": {
"20": 3550249
},
"R2:Right": {
"144": 422,
"145": 3921,
"146": 137570,
"147": 149168,
"35": 1,
"148": 1098902,
"149": 2160257,
"133": 1,
"138": 2,
"139": 2,
"142": 2,
"143": 1
}
},
"lengthDistributions": {
"R2": {
"128": 1098902,
"129": 2160257,
"15": 1,
"113": 1,
"118": 2,
"119": 2,
"122": 2,
"123": 1,
"124": 422,
"125": 3921,
"126": 137570,
"127": 149168
}
},
"costDistributions": {
"0": 3550249
},
"variantDistribution": {
"0": 3550249
}
}
]
],
"costDistributions": {
"0": 3433842,
"5": 109648,
"10": 6759
}
}
}
}
]
}
},
"refineTagsAndSort": {
"type": "refineTagsAndSort",
"commandLine": "--report results/Multi_TRA_FS115_1.refine.report.txt --json-report results/Multi_TRA_FS115_1.refine.report.json results/Multi_TRA_FS115_1.vdjca results/Multi_TRA_FS115_1.refined.vdjca",
"inputFiles": [
"results/Multi_TRA_FS115_1.vdjca"
],
"outputFiles": [
"results/Multi_TRA_FS115_1.refined.vdjca"
],
"version": "4.0.0-432-protocols; built=Tue Oct 11 09:48:35 CEST 2022; rev=2b3b93fc41; lib=repseqio.v2.0",
"correctionReport": {
"inputRecords": 3448498,
"outputRecords": 3302573,
"steps": [
{
"tagName": "UMI",
"inputGroups": 1,
"inputDiversity": 266703,
"inputCount": 3448498,
"coreDiversity": 266674,
"coreCount": 3448469,
"directlyCorrectedDiversity": 129642,
"directlyCorrectedCount": 144398,
"filteredDiversity": 1,
"filteredCount": 1,
"recursivelyCorrected": 6799,
"diversityFilteredByWhitelist": 0,
"outputDiversity": 137060,
"outputCount": 3448497
}
],
"filterReport": {
"type": "filter_groups_report",
"groupingKeys": [
"UMI"
],
"numberOfGroups": 137060,
"numberOfGroupsAccepted": 53937,
"totalWeight": 3448497,
"totalWeightAccepted": 3302573,
"operatorReports": [
{
"operatorReport": {
"type": "generic_hist_report",
"threshold": 8
},
"metricHists": [
{
"bins": [
{
"from": 1,
"to": 1.5848931924611136,
"weight": 58017
},
{
"from": 1.5848931924611136,
"to": 2.51188643150958,
"weight": 9696
},
{
"from": 2.51188643150958,
"to": 3.981071705534973,
"weight": 5234
},
{
"from": 3.981071705534973,
"to": 6.309573444801933,
"weight": 8426
},
{
"from": 6.309573444801933,
"to": 10,
"weight": 4559
},
{
"from": 10,
"to": 15.848931924611142,
"weight": 6605
},
{
"from": 15.848931924611142,
"to": 25.11886431509581,
"weight": 8135
},
{
"from": 25.11886431509581,
"to": 39.810717055349734,
"weight": 8412
},
{
"from": 39.810717055349734,
"to": 63.09573444801933,
"weight": 10494
},
{
"from": 63.09573444801933,
"to": 100,
"weight": 7942
},
{
"from": 100,
"to": 158.48931924611142,
"weight": 6323
},
{
"from": 158.48931924611142,
"to": 251.18864315095823,
"weight": 2185
},
{
"from": 251.18864315095823,
"to": 398.1071705534973,
"weight": 558
},
{
"from": 398.1071705534973,
"to": 630.9573444801937,
"weight": 472
},
{
"from": 630.9573444801937,
"to": 1000,
"weight": 2
}
],
"collectionSpec": {
"log": true,
"binNumber": 0,
"minBinWidth": 0.2
}
}
]
}
]
}
}
},
"assemble": {
"type": "assemblerReport",
"commandLine": "--report results/Multi_TRA_FS115_1.assemble.report.txt --json-report results/Multi_TRA_FS115_1.assemble.report.json results/Multi_TRA_FS115_1.refined.vdjca results/Multi_TRA_FS115_1.clns",
"inputFiles": [
"results/Multi_TRA_FS115_1.refined.vdjca"
],
"outputFiles": [
"results/Multi_TRA_FS115_1.clns"
],
"version": "4.0.0-432-protocols; built=Tue Oct 11 09:48:35 CEST 2022; rev=2b3b93fc41; lib=repseqio.v2.0",
"preCloneAssemblerReport": {
"type": "preCloneAssemblerReport",
"inputGroups": 53937,
"inputAlignments": 3302573,
"clonotypes": 50730,
"clonotypesPerGroup": {
"0": 3239,
"1": 50558,
"2": 86
},
"coreAlignments": 2748073,
"discardedCoreAlignments": 504431,
"empiricallyAssignedAlignments": 8264,
"vjEmpiricallyAssignedAlignments": 0,
"umiEmpiricallyAssignedAlignments": 0,
"gatEmpiricallyAssignedAlignments": 8264,
"empiricalAssignmentConflicts": 0,
"unassignedAlignments": 545221,
"umiConflicts": 86,
"gatConflicts": 4,
"geneConflicts": {
"Variable": 3,
"Joining": 1
},
"coreClonotypesDroppedByTagSuffix": 0,
"coreAlignmentsDroppedByTagSuffix": 0
},
"totalReadsProcessed": 3567679,
"initialClonesCreated": 28046,
"readsDroppedNoTargetSequence": 50069,
"readsDroppedTooShortClonalSequence": 52,
"readsDroppedLowQuality": 0,
"coreReads": 2755073,
"readsDroppedFailedMapping": 1154,
"lowQualityRescued": 58,
"clonesClustered": 88,
"readsClustered": 4756,
"clones": 27957,
"clonesDroppedAsLowQuality": 0,
"clonesPreClustered": 1,
"readsPreClustered": 30,
"readsInClones": 2750375,
"readsInClonesBeforeClustering": 2755131,
"readsDroppedWithLowQualityClones": 0,
"clonalChainUsage": {
"type": "chainUsage",
"chimeras": 0,
"total": 27957,
"chains": {
"TRA": {
"total": 27956,
"nonFunctional": 2833,
"isOOF": 2717,
"hasStops": 116
},
"TRD": {
"total": 1,
"nonFunctional": 1,
"isOOF": 1,
"hasStops": 0
}
}
}
}
}