SMARTer Human BCR IgG IgM H/K/L Profiling Sequencing Kit (Takara Bio Inc.)

============== Align Report ==============
Input file(s): /raw/PRJEB44566_takara_hsa_bcr/FebControl1_R1.fastq.gz,/raw/PRJEB44566_takara_hsa_bcr/FebControl1_R2.fastq.gz
Output file(s): results/FebControl1.vdjca
Version: ; built=Mon Sep 26 10:55:18 CEST 2022; rev=8c998df1ab; lib=repseqio.v2.0
Command line arguments: --report results/FebControl1.align.report.txt --json-report results/FebControl1.align.report.json --preset local:takara-smarter-human-bcr-cdr3 /raw/PRJEB44566_takara_hsa_bcr/FebControl1_R1.fastq.gz /raw/PRJEB44566_takara_hsa_bcr/FebControl1_R2.fastq.gz results/FebControl1.vdjca
Analysis time: 0ns
Total sequencing reads: 584053
Successfully aligned reads: 525390 (89.96%)
Paired-end alignment conflicts eliminated: 42139 (7.21%)
Alignment failed, no hits (not TCR/IG?): 49276 (8.44%)
Alignment failed because of absence of V hits: 2982 (0.51%)
Alignment failed because of absence of J hits: 6044 (1.03%)
No target with both V and J alignments: 361 (0.06%)
Overlapped: 509629 (87.26%)
Overlapped and aligned: 466857 (79.93%)
Alignment-aided overlaps: 22223 (4.76%)
Overlapped and not aligned: 42772 (7.32%)
No CDR3 parts alignments, percent of successfully aligned: 89 (0.02%)
Partial aligned reads, percent of successfully aligned: 2659 (0.51%)
V gene chimeras: 1154 (0.2%)
J gene chimeras: 2 (0%)
IGH chains: 116697 (22.21%)
IGH non-functional: 3925 (3.36%)
IGK chains: 203474 (38.73%)
IGK non-functional: 8958 (4.4%)
IGL chains: 205219 (39.06%)
IGL non-functional: 11257 (5.49%)
Realigned with forced non-floating bound: 193294 (33.1%)
Realigned with forced non-floating right bound in left read: 52153 (8.93%)
Realigned with forced non-floating left bound in right read: 52153 (8.93%)
============== RefineTagsAndSort Report ==============
Input file(s): results/FebControl1.vdjca
Output file(s): results/FebControl1.refined.vdjca
Version: ; built=Mon Sep 26 10:55:18 CEST 2022; rev=8c998df1ab; lib=repseqio.v2.0
Command line arguments: --report results/FebControl1.refine.report.txt --json-report results/FebControl1.refine.report.json results/FebControl1.vdjca results/FebControl1.refined.vdjca
Analysis time: 0ns
Time spent in correction: 0ns
UMI input diversity: 60939
UMI output diversity: 41866 (68.7%)
UMI input reads: 525390
UMI output count: 522239 (99.4%)
UMI mean reads per tag: 8.62
UMI input core diversity: 48831 (80.13%)
UMI input core reads: 513049 (97.65%)
UMI directly corrected diversity: 15939 (26.16%)
UMI directly corrected reads: 16711 (3.18%)
UMI diversity filtered by tag quality: 3134 (5.14%)
UMI reads filtered by tag quality: 3151 (0.6%)
UMI diversity filtered by whitelist: 0 (0%)
UMI recursively corrected: 878
Number of output records: 487187 (92.73%)
Filter report:
  Number of groups: 41866
  Number of groups accepted: 15113 (36.1%)
  Total records weight: 522239.0
  Records weight accepted: 487187.0 (93.29%)
  Operator #0:
    Effective threshold: 6.0
============== Assemble Report ==============
Input file(s): results/FebControl1.refined.vdjca
Output file(s): results/FebControl1.clns
Version: ; built=Mon Sep 26 10:55:18 CEST 2022; rev=8c998df1ab; lib=repseqio.v2.0
Command line arguments: --report results/FebControl1.assemble.report.txt --json-report results/FebControl1.assemble.report.json results/FebControl1.refined.vdjca results/FebControl1.clns
Analysis time: 0ns
Number of input groups: 15113
Number of input alignments: 487187
Number of output pre-clonotypes: 14993
Number of clonotypes per group:
  0: + 89 (0.59%) = 89 (0.59%)
  1: + 14965 (99.32%) = 15054 (99.91%)
  2: + 14 (0.09%) = 15068 (100%)
Number of core alignments: 474527 (97.4%)
Discarded core alignments: 4683 (0.99%)
Empirically assigned alignments: 5590 (1.15%)
Empirical assignment conflicts: 0 (0%)
UMI+VJ-gene empirically assigned alignments: 5590 (1.15%)
VJ-gene empirically assigned alignments: 0 (0%)
UMI empirically assigned alignments: 0 (0%)
Number of ambiguous UMIs: 14
Number of ambiguous V-genes: 5
Number of ambiguous J-genes: 3
Number of ambiguous UMI+V/J-gene combinations: 8
Unassigned alignments: 5618 (1.15%)
Final clonotype count: 8448
Average number of reads per clonotype: 56.69
Reads used in clonotypes, percent of total: 478906 (82%)
Reads used in clonotypes before clustering, percent of total: 479893 (82.17%)
Number of reads used as a core, percent of used: 479850 (99.99%)
Mapped low quality reads, percent of used: 43 (0.01%)
Reads clustered in PCR error correction, percent of used: 987 (0.21%)
Reads pre-clustered due to the similar VJC-lists, percent of used: 10879 (2.27%)
Reads dropped due to the lack of a clone sequence, percent of total: 7977 (1.37%)
Reads dropped due to a too short clonal sequence, percent of total: 0 (0%)
Reads dropped due to low quality, percent of total: 3 (0%)
Reads dropped due to failed mapping, percent of total: 10 (0%)
Reads dropped with low quality clones, percent of total: 214 (0.04%)
Clonotypes eliminated by PCR error correction: 60
Clonotypes dropped as low quality: 3
Clonotypes pre-clustered due to the similar VJC-lists: 299
IGH chains: 1533 (18.15%)
IGH non-functional: 43 (2.8%)
IGK chains: 3432 (40.62%)
IGK non-functional: 209 (6.09%)
IGL chains: 3483 (41.23%)
IGL non-functional: 233 (6.69%)

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        "directlyCorrectedCount": 16711,
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  "type": "assemblerReport",
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  "version": "; built=Mon Sep 26 10:55:18 CEST 2022; rev=8c998df1ab; lib=repseqio.v2.0",
  "preCloneAssemblerReport": {
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