============== Align Report ============== ============== Align Report ============== Total sequencing reads: 913538 Successfully aligned reads: 888254 (97.23%) Alignment failed: no hits (not TCR/IG?): 13909 (1.52%) Alignment failed: absence of V hits: 845 (0.09%) Alignment failed: absence of J hits: 9805 (1.07%) Alignment failed: no target with both V and J alignments: 725 (0.08%) Overlapped: 731723 (80.1%) Overlapped and aligned: 711536 (77.89%) Overlapped and not aligned: 20187 (2.21%) Alignment-aided overlaps, percent of overlapped and aligned: 3526 (0.5%) No CDR3 parts alignments, percent of successfully aligned: 176 (0.02%) Partial aligned reads, percent of successfully aligned: 3490 (0.39%) Chimeras: 9 (0%) V gene chimeras: 2911 (0.32%) J gene chimeras: 1 (0%) Paired-end alignment conflicts eliminated: 70705 (7.74%) Realigned with forced non-floating bound: 370682 (40.58%) Realigned with forced non-floating right bound in left read: 82102 (8.99%) Realigned with forced non-floating left bound in right read: 82102 (8.99%) IGH chains: 177773 (20.01%) IGH non-functional: 2174 (1.22%) IGK chains: 286240 (32.23%) IGK non-functional: 4539 (1.59%) IGL chains: 276057 (31.08%) IGL non-functional: 4967 (1.8%) TRA chains: 70696 (7.96%) TRA non-functional: 4994 (7.06%) TRB chains: 77478 (8.72%) TRB non-functional: 1793 (2.31%) TRG chains: 1 (0%) TRG non-functional: 0 (0%) Trimming report: R1 reads trimmed left: 224 (0.02%) R1 reads trimmed right: 227302 (24.88%) Average R1 nucleotides trimmed left: 0.03396903029759025 Average R1 nucleotides trimmed right: 1.5750215097784657 R2 reads trimmed left: 468 (0.05%) R2 reads trimmed right: 728608 (79.76%) Average R2 nucleotides trimmed left: 0.03046507096584926 Average R2 nucleotides trimmed right: 27.645503525852234 Tag parsing report: Total reads: 913538 Matched reads: 913538 (100%) Projection +R1 +R2: 913538 (100%) For variant 0: For projection [1, 2]: R1:Left position: 7 R1:Right position: 35~299: + 160374 (17.56%) = 160374 (17.56%) 300: + 753164 (82.44%) = 913538 (100%) R2:Left position: 16 R2:Right position: 47~299: + 158097 (17.31%) = 158097 (17.31%) 300: + 755441 (82.69%) = 913538 (100%) UMI:Left position: 0 Variants: 0 Cost: 0 R1 length: 28~292: + 160374 (17.56%) = 160374 (17.56%) 293: + 753164 (82.44%) = 913538 (100%) R2 length: 31~283: + 158097 (17.31%) = 158097 (17.31%) 284: + 755441 (82.69%) = 913538 (100%) UMI length: 12 ============== RefineTagsAndSort Report ============== ============== RefineTagsAndSort Report ============== Time spent in correction: 0ns Number of input records: 888249 Number of output records: 811429 (91.35%) UMI correction report: UMI input diversity: 324823 UMI output diversity: 299306 (92.14%) UMI input reads: 888249 UMI output reads: 881574 (99.25%) UMI mean reads per tag: 2.73 UMI input core diversity: 303279 (93.37%) UMI input core reads: 866542 (97.56%) UMI directly corrected diversity: 18953 (5.83%) UMI directly corrected reads: 19041 (2.14%) UMI diversity filtered by tag quality: 6564 (2.02%) UMI reads filtered by tag quality: 6675 (0.75%) UMI diversity filtered by whitelist: 0 (0%) UMI recursively corrected: 223 Filter report: Number of groups: 299306 Number of groups accepted: 229161 (76.56%) Total records weight: 881574 Records weight accepted: 811429 (92.04%) Operator #0: Effective threshold: 2.0 Nested thresholds: #0: 2 #1: 2 ============== Assemble Report ============== ============== Assemble Report ============== Final clonotype count: 54058 Reads used in clonotypes, percent of total: 601054 (65.79%) Average number of reads per clonotype: 11.12 Reads dropped due to the lack of a clone sequence, percent of total: 164684 (18.03%) Reads dropped due to a too short clonal sequence, percent of total: 0 (0%) Reads dropped due to low quality, percent of total: 0 (0%) Reads dropped due to failed mapping, percent of total: 110938 (12.14%) Reads dropped with low quality clones, percent of total: 0 (0%) Reads used in clonotypes before clustering, percent of total: 602878 (65.99%) Number of reads used as a core, percent of used: 586880 (97.35%) Mapped low quality reads, percent of used: 15998 (2.65%) Reads clustered in PCR error correction, percent of used: 1824 (0.3%) Reads pre-clustered due to the similar VJC-lists, percent of used: 2488 (0.41%) Clonotypes dropped as low quality: 0 Clonotypes eliminated by PCR error correction: 411 Clonotypes pre-clustered due to the similar VJC-lists: 355 Clones dropped in post filtering: 0 (0%) Reads dropped in post filtering: 0.0 (0%) Alignments filtered by tag prefix: 0 (0%) IGH chains: 4714 (8.72%) IGH non-functional: 21 (0.45%) IGK chains: 19623 (36.3%) IGK non-functional: 497 (2.53%) IGL chains: 15816 (29.26%) IGL non-functional: 516 (3.26%) TRA chains: 6233 (11.53%) TRA non-functional: 549 (8.81%) TRB chains: 7671 (14.19%) TRB non-functional: 135 (1.76%) Pre-clone assembler report: Number of input groups: 229161 Number of input groups with no assembling feature: 21932 Number of input alignments: 811429 Number of alignments with assembling feature: 646745 (79.7%) Number of output pre-clones: 209338 Number of pre-clonotypes per group: 0: + 707 (0.34%) = 707 (0.34%) 1: + 203722 (98.31%) = 204429 (98.65%) 2: + 2784 (1.34%) = 207213 (99.99%) 3: + 16 (0.01%) = 207229 (100%) Number of assembling feature sequences in groups with zero pre-clonotypes: 3096 Number of dropped pre-clones by tag suffix conflict: 0 Number of dropped alignments by tag suffix conflict: 0 Number of core alignments: 632546 (77.95%) Discarded core alignments: 14199 (2.24%) Empirically assigned alignments: 81270 (10.02%) Empirical assignment conflicts: 0 (0%) Tag+VJ-gene empirically assigned alignments: 81270 (10.02%) VJ-gene empirically assigned alignments: 0 (0%) Tag empirically assigned alignments: 0 (0%) Number of ambiguous groups: 2800 Number of ambiguous V-genes: 6 Number of ambiguous J-genes: 236 Number of ambiguous tag+V/J-gene combinations: 242 Ignored non-productive alignments: 0 (0%) Unassigned alignments: 31440 (3.87%)