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/fh/fast/matsen_e/dralph/code/partis-dev/bin/partis cache-parameters --infname /fh/fast/matsen_e/data/chaim-iarc/08248_partis.yaml --print-git-commit --locus igh --parameter-dir /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248 --sw-cachefname /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/sw-cache.yaml --plotdir /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/plots --debug-allele-finding --n-procs 15
commit: a04abc73925f14fcd0125aa6ad6687154c39f590
tag: v0.15.0 (well, 133 commits ahead of)
note: running on a lot of sequences (238759) without setting --outfname. Which is ok, but there will be no persistent record of the results (except the parameter directory).
caching parameters
vsearch: 186601 / 238759 v annotations (52158 failed) with 174 v genes in 15.2 sec
removing least likely genes with total counts 186601.0
[94mv[0m groups separated by 6 snps (-: same group as previous kept gene)
genes to keep counts removed genes (snps counts)
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[94mnone[0m - (0 15) (3 3.7) [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m05[0m [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m03[0m
[94mnone[0m - (0 10) [95mh[0m[91mv[0m[95m1[0m[95m-45[0m[93m02[0m
[94mnone[0m - (0 9.7) [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m10[0m
[94mnone[0m - (0 5.8) (2 4.3) (1 3.3) [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m04[0m [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m02[0m [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m01[0m
[94mnone[0m - (0 4.5) [95mh[0m[91mv[0m[95m3[0m[95m-11[0m[93m06[0m
[94mnone[0m - (0 3.6) [95mh[0m[91mv[0m[95m4[0m[95m-30-4[0m[93m02[0m
[94mnone[0m - (0 3.3) [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m11[0m
[94mnone[0m - (0 3.2) [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m03[0m
[94mnone[0m - (0 3.1) [95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m05[0m
[94mnone[0m - (0 3.0) [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m10[0m
[94mnone[0m - (0 1.7) [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m09[0m
[94mnone[0m - (0 1.0) [95mh[0m[91mv[0m[95m3[0m[95m-NL1[0m[93m01[0m
[94mnone[0m - (0 1.0) [95mh[0m[91mv[0m[95m3[0m[95m-15[0m[93m03[0m
keeping 39 / 204 v genes
smith-waterman (new-allele fitting)
vsearch: 186583 / 238759 v annotations (52176 failed) with 39 v genes in 49.2 sec
running 15 procs for 238759 seqs
running 18 procs for 95331 seqs
info for 181692 / 238759 = 0.761 (57067 failed)
[91mwarning[0m smith-waterman step failed to find alignments for a large fraction of input sequences (see previous line) [91mnote:[0m maybe need to take reverse complement? (partis only searches in forward direction)
kept 89351 (0.374) unproductive
removed 4324 / 181692 = 0.02 duplicate sequences after trimming framework insertions (leaving 177368)
water time: 724.7 (ig-sw 240.6 processing 147.2)
allele finding
excluding 19 / 39 genes whose reads are too short (adjust with --min-allele-finding-gene-length)
total clones representatives
[95mh[0m[91mv[0m[95m1[0m[95m-46[0m[93m01[0m 2698 1815 2034
[95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m 5096 3776 4326
[95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m 2397 1842 1842
[95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m01[0m 1878 974 1533
[95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m 704 357 357
[95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m01[0m 3228 1796 2470
[95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m 9642 4942 5994
[95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m03[0m 4399 2491 3025
[95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m04[0m 808 392 549
[95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m 5893 3038 3582
[95mh[0m[91mv[0m[95m3[0m[95m-7[0m[93m01[0m 4849 2921 3345
[95mh[0m[91mv[0m[95m3[0m[95m-74[0m[93m01[0m 2826 1439 1509
[95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m01[0m 2428 1360 2045
[95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m03[0m 1384 760 1099
[95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m 16563 6846 12038
[95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m 32812 14423 21224
[95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m02[0m 2487 1071 1629
[95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m 11752 5290 7564
[95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m02[0m 8367 4055 5587
[95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m 4278 2703 2937
84689 seqs chosen to represent 62291 clones with 124489 total seqs
v mutations:
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
772 184 36 87 50 72 179 119 57 33 54 35 53 34 61 18 26 30 8 5 82 30 5 4 [95mh[0m[91mv[0m[95m1[0m[95m-46[0m[93m01[0m
1892 1269 177 444 66 32 34 77 40 18 74 71 28 21 15 9 2 13 16 11 8 5 3 1 [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m
0 1077 180 37 55 44 34 39 33 21 17 34 35 84 22 21 10 30 36 5 8 10 7 3 [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m
950 250 38 39 25 31 34 17 49 14 17 10 10 10 9 15 3 3 0 2 0 3 3 1 [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m01[0m
0 0 111 43 24 38 24 27 24 9 11 9 11 7 8 2 3 2 1 2 1 0 0 0 [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m
1199 338 65 77 59 72 41 71 60 71 73 57 37 36 41 32 73 18 10 9 15 5 3 8 [95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m01[0m
1714 1288 161 106 106 140 152 143 208 186 161 169 184 200 180 115 120 121 103 102 104 88 77 66 [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m
1156 301 97 128 126 147 108 83 91 110 113 119 62 70 26 50 62 18 29 67 14 22 3 23 [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m03[0m
277 43 21 20 19 5 20 22 15 15 12 23 7 1 12 10 5 15 2 0 1 1 0 3 [95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m04[0m
981 298 84 41 136 450 203 123 90 98 98 78 101 109 172 69 109 67 74 70 40 25 53 13 [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m
1037 221 145 121 160 116 189 165 176 216 157 117 119 61 96 87 31 39 20 13 8 25 17 9 [95mh[0m[91mv[0m[95m3[0m[95m-7[0m[93m01[0m
256 59 43 51 47 71 62 36 100 113 61 52 68 92 89 50 74 72 37 20 21 18 8 9 [95mh[0m[91mv[0m[95m3[0m[95m-74[0m[93m01[0m
1331 336 68 37 30 22 25 27 20 15 15 16 22 20 10 7 10 6 5 3 11 3 5 1 [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m01[0m
736 115 26 23 24 15 35 22 4 13 14 12 2 8 7 13 6 5 7 8 0 1 3 0 [95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m03[0m
6954 2269 510 305 378 296 250 166 134 86 134 95 86 64 61 46 49 53 32 14 13 14 13 16 [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
11461 3072 631 387 437 398 380 333 392 388 390 454 357 265 276 388 194 231 163 183 156 89 96 103 [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m
955 214 39 33 34 38 23 18 23 54 20 27 23 10 14 15 11 11 16 25 15 1 9 1 [95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m02[0m
3948 1427 180 83 142 115 112 121 117 113 125 124 139 134 122 95 62 107 103 60 48 25 40 22 [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
2908 774 165 127 168 110 108 165 159 103 93 87 105 80 99 81 49 33 34 48 31 23 24 13 [95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m02[0m
671 567 178 174 149 232 162 162 154 94 78 66 48 77 39 9 27 17 9 13 4 1 3 3 [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m
sequence counts:
excluded excluded excluded included actually
>23 mutations 5p del (>N bases) 3p del (>N bases) total seqs clones used
49 8 (0) 27 (39) 2698 1815 2034 [95mh[0m[91mv[0m[95m1[0m[95m-46[0m[93m01[0m
55 9 (0) 42 (8) 5096 3776 4326 [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m
177 7 (0) 21 (27) 2397 1842 1842 [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m
34 4 (37) 17 (36) 1878 974 1533 [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m01[0m
25 7 (21) 7 (71) 704 357 357 [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m
97 10 (0) 13 (7) 3228 1796 2470 [95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m01[0m
848 13 (0) 84 (8) 9642 4942 5994 [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m
130 44 (8) 2 (101) 4399 2491 3025 [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m03[0m
22 2 (39) 8 (37) 808 392 549 [95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m04[0m
352 3 (0) 57 (10) 5893 3038 3582 [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m
224 18 (0) 40 (99) 4849 2921 3345 [95mh[0m[91mv[0m[95m3[0m[95m-7[0m[93m01[0m
325 9 (0) 12 (59) 2826 1439 1509 [95mh[0m[91mv[0m[95m3[0m[95m-74[0m[93m01[0m
19 0 (0) 21 (8) 2428 1360 2045 [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m01[0m
21 9 (82) 8 (23) 1384 760 1099 [95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m03[0m
318 2 (0) 154 (6) 16563 6846 12038 [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
1424 12 (0) 320 (7) 32812 14423 21224 [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m
220 3 (0) 27 (39) 2487 1071 1629 [95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m02[0m
466 3 (0) 110 (6) 11752 5290 7564 [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
249 5 (0) 65 (6) 8367 4055 5587 [95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m02[0m
77 25 (29) 44 (65) 4278 2703 2937 [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m
[94mtry 0[0m: looking for new alleles among 20 genes (0 genes didn't have enough counts)
[95mh[0m[91mv[0m[95m1[0m[95m-46[0m[93m01[0m 2034 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
6 snps
[93m101[0m 3.61 10. / 2.84 0 / 772 2 / 184 2 / 36 4 / 87 0 / 50 10 / 72 79 / 179 54 / 119 26 / 57 11 / 33 16 / 54 8 / 35 27 / 53 9 / 34 32 / 61 3 / 18
[93m196[0m 2.91 5.27 / 1.81 0 / 772 4 / 184 0 / 36 1 / 87 0 / 50 0 / 72 33 / 179 29 / 119 4 / 57 4 / 33 9 / 54 6 / 35 3 / 53 0 / 34 3 / 61 1 / 18
99 1.86 2.70 / 1.45 0 / 772 0 / 184 0 / 36 0 / 87 0 / 50 3 / 72 27 / 179 12 / 119 10 / 57 0 / 33 4 / 54 4 / 35 3 / 53 1 / 34 8 / 61 2 / 18
251 1.05 3.49 / 3.33 0 / 772 0 / 184 0 / 36 0 / 87 3 / 50 0 / 72 30 / 179 6 / 119 0 / 57 0 / 33 0 / 54 0 / 35 1 / 53 9 / 34 4 / 61 0 / 18
207 0.93 3.81 / 4.10 0 / 772 0 / 184 0 / 36 0 / 87 0 / 50 0 / 72 13 / 179 5 / 119 0 / 57 0 / 33 0 / 54 0 / 35 0 / 53 0 / 34 25 / 61 1 / 18
38 0.90 3.36 / 3.72 0 / 772 0 / 184 0 / 36 0 / 87 0 / 50 1 / 72 16 / 179 2 / 119 0 / 57 0 / 33 0 / 54 0 / 35 0 / 53 0 / 34 22 / 61 0 / 18
snps min ratio
6 0.90 min snp ratio 0.90 too small (less than 2.25)
[95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m 4326 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
3 snps
[93m169[0m 26. 459. / 18. 0 / 1892 2 / 1269 6 / 177 411 / 444 42 / 66 5 / 32 8 / 34 44 / 77 31 / 40 6 / 18 27 / 74 32 / 71 3 / 28
[93m219[0m 24. 425. / 18. 0 / 1892 3 / 1269 1 / 177 409 / 444 48 / 66 6 / 32 7 / 34 44 / 77 11 / 40 3 / 18 26 / 74 43 / 71 4 / 28
[93m162[0m 20. 478. / 24. 0 / 1892 0 / 1269 9 / 177 411 / 444 42 / 66 5 / 32 6 / 34 43 / 77 10 / 40 1 / 18 24 / 74 41 / 71 4 / 28
7 snps
[93m155[0m 2.32 2.74 / 1.18 0 / 1892 1 / 1269 0 / 177 0 / 444 0 / 66 2 / 32 0 / 34 14 / 77 3 / 40 0 / 18 5 / 74 14 / 71 2 / 28 0 / 21 0 / 15 0 / 9 0 / 2
206 1.46 3.89 / 2.66 0 / 1892 1 / 1269 3 / 177 0 / 444 0 / 66 0 / 32 0 / 34 11 / 77 2 / 40 1 / 18 7 / 74 3 / 71 1 / 28 10 / 21 7 / 15 2 / 9 0 / 2
224 1.32 2.57 / 1.94 0 / 1892 0 / 1269 0 / 177 0 / 444 0 / 66 0 / 32 0 / 34 23 / 77 2 / 40 2 / 18 0 / 74 2 / 71 0 / 28 0 / 21 0 / 15 1 / 9 0 / 2
159 1.19 2.81 / 2.35 0 / 1892 0 / 1269 0 / 177 0 / 444 0 / 66 0 / 32 0 / 34 14 / 77 3 / 40 0 / 18 3 / 74 0 / 71 3 / 28 7 / 21 1 / 15 2 / 9 1 / 2
166 1.02 2.96 / 2.91 0 / 1892 0 / 1269 0 / 177 0 / 444 0 / 66 0 / 32 0 / 34 23 / 77 0 / 40 2 / 18 0 / 74 1 / 71 0 / 28 0 / 21 5 / 15 1 / 9 0 / 2
149 1.01 2.80 / 2.77 0 / 1892 3 / 1269 1 / 177 0 / 444 0 / 66 0 / 32 0 / 34 12 / 77 2 / 40 0 / 18 0 / 74 3 / 71 7 / 28 2 / 21 7 / 15 1 / 9 0 / 2
201 0.99 2.82 / 2.85 0 / 1892 4 / 1269 1 / 177 0 / 444 1 / 66 0 / 32 0 / 34 14 / 77 4 / 40 0 / 18 1 / 74 0 / 71 2 / 28 0 / 21 7 / 15 1 / 9 1 / 2
snps min ratio
3 20. candidate
7 0.99 min snp ratio 0.99 too small (less than 2.25)
exact sequence in glfo under name [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m10[0m
[91mnew[0m [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m10[0m separated from [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m by 3 snps at: 162 (T --> C) 169 (C --> T) 219 (G --> A)
[95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m 1842 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
1 snp
[93m209[0m 2e+05 6e+04 / 0.31 0 / 0 1077 / 1077 180 / 180 37 / 37 55 / 55 43 / 44 32 / 34 39 / 39 33 / 33 21 / 21 17 / 17
snps min ratio
1 2e+05 candidate
no equivalent gene for [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02+G209T[0m nearest is [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m (1 snp, 0 indels):
CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGCTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCAT[91mG[0mACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02+G209T[0m
CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGCTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m
[91mnew[0m [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02+G209T[0m separated from [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m by 1 snp at: 209 (G --> T)
[95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m01[0m 1533 counts
[95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m 357 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
2 snps
[93m147[0m 2e+04 576. / 0.03 0 / 0 0 / 0 110 / 111 43 / 43 24 / 24 38 / 38 24 / 24 27 / 27 24 / 24 9 / 9 11 / 11 9 / 9
[93m102[0m 15. 13. / 0.86 0 / 0 0 / 0 74 / 111 22 / 43 17 / 24 25 / 38 16 / 24 22 / 27 19 / 24 8 / 9 8 / 11 8 / 9
snps min ratio
2 15. candidate
[94mequivalent[0m gene [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m11[0m with same cpos in glfo for [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10+C102T.A147C[0m (blue bases are not considered):
[94mCAGGTCACCTTGAAGGAGTCT[0mGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTAC[7mTGT[0m[94mAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC[0m [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10+C102T.A147C[0m
[94mCGGGTCACCTTGAGGGAGTCT[0mGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTAC[7mTGT[0m[94mAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC[0m [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m11[0m
[91mnew[0m [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m11[0m separated from [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m by 2 snps at: 102 (C --> T) 147 (A --> C)
[95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m01[0m 2470 counts
[95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m 5994 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
1 snp
[93m 12[0m 21. 175. / 8.13 0 / 1714 733 / 1288 86 / 161 23 / 106 42 / 106 58 / 140 42 / 152 43 / 143 76 / 208 54 / 186 47 / 161
3 snps
[93m148[0m 37. 76. / 2.08 0 / 1714 0 / 1288 7 / 161 30 / 106 43 / 106 49 / 140 66 / 152 63 / 143 105 / 208 82 / 186 68 / 161 80 / 169 81 / 184
[93m234[0m 3.41 6.07 / 1.78 0 / 1714 0 / 1288 0 / 161 11 / 106 3 / 106 5 / 140 9 / 152 22 / 143 12 / 208 17 / 186 15 / 161 14 / 169 19 / 184
152 2.24 2.56 / 1.14 0 / 1714 0 / 1288 0 / 161 9 / 106 2 / 106 4 / 140 8 / 152 4 / 143 7 / 208 5 / 186 7 / 161 14 / 169 9 / 184
snps min ratio
1 21. candidate
3 2.24 min snp ratio 2.24 too small (less than 2.25)
exact sequence in glfo under name [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m01[0m
[91mnew[0m [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m01[0m separated from [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m by 1 snp at: 12 (G --> T)
[95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m03[0m 3025 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
4 snps
[93m172[0m 2.66 4.06 / 1.53 0 / 1156 0 / 301 0 / 97 4 / 128 17 / 126 14 / 147 14 / 108 11 / 83 18 / 91 22 / 110 27 / 113 24 / 119 13 / 62 31 / 70
90 1.11 4.50 / 4.04 0 / 1156 0 / 301 3 / 97 4 / 128 22 / 126 19 / 147 4 / 108 12 / 83 16 / 91 6 / 110 8 / 113 12 / 119 4 / 62 19 / 70
83 1.02 2.17 / 2.13 0 / 1156 2 / 301 1 / 97 2 / 128 15 / 126 11 / 147 3 / 108 10 / 83 7 / 91 9 / 110 13 / 113 19 / 119 17 / 62 13 / 70
17 0.87 3.38 / 3.90 0 / 1156 2 / 301 0 / 97 1 / 128 16 / 126 2 / 147 0 / 108 5 / 83 2 / 91 0 / 110 7 / 113 11 / 119 8 / 62 0 / 70
snps min ratio
4 0.87 min snp ratio 0.87 too small (less than 2.25)
[95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m04[0m 549 counts
[95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m 3582 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
5 snps
[93m 23[0m 5.66 162. / 29. 0 / 981 2 / 298 0 / 84 0 / 41 3 / 136 395 / 450 90 / 203 34 / 123 29 / 90 40 / 98 44 / 98 17 / 78 41 / 101 44 / 109 71 / 172
[93m 77[0m 5.51 142. / 26. 0 / 981 0 / 298 2 / 84 2 / 41 8 / 136 394 / 450 93 / 203 41 / 123 33 / 90 43 / 98 46 / 98 20 / 78 63 / 101 62 / 109 91 / 172
[93m 33[0m 5.47 159. / 29. 0 / 981 0 / 298 0 / 84 0 / 41 7 / 136 395 / 450 92 / 203 32 / 123 28 / 90 43 / 98 44 / 98 19 / 78 42 / 101 41 / 109 74 / 172
[93m272[0m 5.43 159. / 29. 0 / 981 0 / 298 1 / 84 0 / 41 5 / 136 394 / 450 92 / 203 32 / 123 26 / 90 41 / 98 44 / 98 18 / 78 41 / 101 44 / 109 69 / 172
[93m195[0m 5.17 151. / 29. 0 / 981 3 / 298 0 / 84 0 / 41 6 / 136 394 / 450 92 / 203 32 / 123 27 / 90 41 / 98 44 / 98 17 / 78 41 / 101 44 / 109 69 / 172
snps min ratio
5 5.17 candidate
exact sequence in glfo under name [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m01[0m
[91mnew[0m [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m01[0m separated from [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m by 5 snps at: 23 (A --> G) 33 (A --> G) 77 (G --> A) 195 (C --> A) 272 (C --> T)
[95mh[0m[91mv[0m[95m3[0m[95m-7[0m[93m01[0m 3345 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
1 snp
9 1.04 3.72 / 3.59 0 / 1037 10 / 221 15 / 145 8 / 121 12 / 160 11 / 116 7 / 189 25 / 165 27 / 176 34 / 216 19 / 157
3 snps
92 1.72 7.28 / 4.24 0 / 1037 6 / 221 3 / 145 25 / 121 43 / 160 22 / 116 60 / 189 57 / 165 80 / 176 65 / 216 70 / 157 66 / 117 40 / 119
82 1.38 2.73 / 1.98 0 / 1037 3 / 221 0 / 145 9 / 121 8 / 160 16 / 116 26 / 189 23 / 165 25 / 176 20 / 216 32 / 157 20 / 117 21 / 119
173 1.22 3.55 / 2.92 0 / 1037 0 / 221 1 / 145 13 / 121 15 / 160 17 / 116 9 / 189 12 / 165 29 / 176 24 / 216 17 / 157 26 / 117 22 / 119
snps min ratio
1 1.04 min snp ratio 1.04 too small (less than 2.25)
3 1.22 min snp ratio 1.22 too small (less than 2.25)
[95mh[0m[91mv[0m[95m3[0m[95m-74[0m[93m01[0m 1509 counts
[95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m01[0m 2045 counts
[95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m03[0m 1099 counts
[95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m 12038 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
1 snp
[93m270[0m 4.45 5.65 / 1.27 0 / 6954 50 / 2269 6 / 510 3 / 305 3 / 378 1 / 296 5 / 250 0 / 166 1 / 134 0 / 86 2 / 134
1 snp
[93m116[0m 3.49 2.58 / 0.74 0 / 6954 20 / 2269 8 / 510 4 / 305 6 / 378 6 / 296 4 / 250 3 / 166 0 / 134 1 / 86 1 / 134
4 snps
[93m227[0m 3.37 14. / 4.01 0 / 6954 4 / 2269 15 / 510 20 / 305 52 / 378 31 / 296 27 / 250 26 / 166 28 / 134 10 / 86 29 / 134 18 / 95 11 / 86 8 / 64
[93m131[0m 3.33 12. / 3.73 0 / 6954 18 / 2269 13 / 510 3 / 305 89 / 378 63 / 296 30 / 250 19 / 166 8 / 134 11 / 86 16 / 134 8 / 95 10 / 86 11 / 64
117 1.23 3.41 / 2.78 0 / 6954 26 / 2269 13 / 510 6 / 305 24 / 378 12 / 296 18 / 250 2 / 166 6 / 134 4 / 86 7 / 134 12 / 95 3 / 86 8 / 64
230 1.18 2.55 / 2.17 0 / 6954 11 / 2269 6 / 510 3 / 305 23 / 378 14 / 296 11 / 250 5 / 166 5 / 134 1 / 86 9 / 134 7 / 95 16 / 86 3 / 64
5 snps
104 1.58 4.25 / 2.69 0 / 6954 26 / 2269 5 / 510 14 / 305 13 / 378 43 / 296 27 / 250 26 / 166 8 / 134 18 / 86 13 / 134 9 / 95 13 / 86 5 / 64 14 / 61
62 1.57 3.97 / 2.53 0 / 6954 8 / 2269 13 / 510 12 / 305 7 / 378 38 / 296 18 / 250 8 / 166 7 / 134 5 / 86 5 / 134 2 / 95 6 / 86 8 / 64 4 / 61
180 1.28 3.51 / 2.75 0 / 6954 12 / 2269 10 / 510 2 / 305 6 / 378 23 / 296 6 / 250 2 / 166 17 / 134 3 / 86 5 / 134 1 / 95 3 / 86 0 / 64 1 / 61
280 1.18 4.32 / 3.65 0 / 6954 2 / 2269 14 / 510 6 / 305 4 / 378 19 / 296 6 / 250 18 / 166 4 / 134 3 / 86 4 / 134 12 / 95 5 / 86 1 / 64 7 / 61
215 1.15 2.63 / 2.28 0 / 6954 8 / 2269 3 / 510 2 / 305 4 / 378 22 / 296 5 / 250 0 / 166 0 / 134 0 / 86 0 / 134 2 / 95 5 / 86 1 / 64 0 / 61
6 snps
[93m201[0m 2.38 5.59 / 2.35 0 / 6954 3 / 2269 1 / 510 6 / 305 1 / 378 2 / 296 25 / 250 12 / 166 19 / 134 6 / 86 6 / 134 4 / 95 6 / 86 2 / 64 7 / 61 13 / 46
90 1.60 3.43 / 2.14 0 / 6954 7 / 2269 2 / 510 10 / 305 2 / 378 5 / 296 23 / 250 15 / 166 4 / 134 6 / 86 5 / 134 13 / 95 10 / 86 6 / 64 6 / 61 3 / 46
8 1.60 4.85 / 3.04 0 / 6954 13 / 2269 10 / 510 4 / 305 2 / 378 9 / 296 26 / 250 20 / 166 6 / 134 4 / 86 25 / 134 14 / 95 10 / 86 6 / 64 11 / 61 3 / 46
9 1.14 4.25 / 3.72 0 / 6953 5 / 2269 3 / 510 0 / 305 3 / 378 6 / 296 33 / 250 9 / 166 3 / 134 1 / 86 22 / 134 2 / 95 2 / 86 3 / 64 6 / 61 2 / 46
96 1.09 3.17 / 2.90 0 / 6954 7 / 2269 6 / 510 0 / 305 12 / 378 2 / 296 18 / 250 5 / 166 8 / 134 9 / 86 0 / 134 4 / 95 6 / 86 2 / 64 1 / 61 2 / 46
146 0.90 3.27 / 3.64 0 / 6954 36 / 2269 10 / 510 12 / 305 40 / 378 10 / 296 25 / 250 18 / 166 9 / 134 7 / 86 28 / 134 15 / 95 26 / 86 16 / 64 8 / 61 11 / 46
8 snps
[93m156[0m 2.35 4.20 / 1.79 0 / 6954 6 / 2269 2 / 510 2 / 305 9 / 378 9 / 296 5 / 250 4 / 166 18 / 134 11 / 86 12 / 134 18 / 95 16 / 86 9 / 64 9 / 61 9 / 46 1 / 49 5 / 53
202 1.57 3.67 / 2.34 0 / 6954 14 / 2269 4 / 510 11 / 305 14 / 378 4 / 296 9 / 250 9 / 166 25 / 134 4 / 86 12 / 134 3 / 95 7 / 86 1 / 64 7 / 61 2 / 46 0 / 49 1 / 53
149 1.52 4.93 / 3.24 0 / 6954 0 / 2269 0 / 510 17 / 305 6 / 378 1 / 296 2 / 250 4 / 166 17 / 134 5 / 86 5 / 134 11 / 95 4 / 86 13 / 64 6 / 61 3 / 46 4 / 49 1 / 53
14 1.40 2.64 / 1.89 0 / 6954 11 / 2269 5 / 510 9 / 305 8 / 378 16 / 296 9 / 250 9 / 166 22 / 134 6 / 86 15 / 134 8 / 95 11 / 86 8 / 64 13 / 61 4 / 46 1 / 49 9 / 53
71 1.24 4.07 / 3.30 0 / 6954 9 / 2269 1 / 510 2 / 305 6 / 378 4 / 296 2 / 250 2 / 166 23 / 134 8 / 86 6 / 134 12 / 95 2 / 86 11 / 64 3 / 61 1 / 46 13 / 49 8 / 53
211 1.10 3.58 / 3.25 0 / 6954 0 / 2269 0 / 510 4 / 305 1 / 378 5 / 296 7 / 250 5 / 166 24 / 134 0 / 86 5 / 134 7 / 95 6 / 86 2 / 64 4 / 61 1 / 46 0 / 49 0 / 53
135 1.02 2.52 / 2.47 0 / 6954 6 / 2269 0 / 510 0 / 305 1 / 378 3 / 296 2 / 250 8 / 166 22 / 134 3 / 86 2 / 134 1 / 95 6 / 86 3 / 64 1 / 61 2 / 46 3 / 49 0 / 53
134 0.97 2.74 / 2.82 0 / 6954 10 / 2269 1 / 510 0 / 305 0 / 378 0 / 296 1 / 250 0 / 166 23 / 134 2 / 86 1 / 134 0 / 95 2 / 86 4 / 64 4 / 61 2 / 46 2 / 49 0 / 53
snps min ratio
1 4.45 candidate
1 3.49 candidate
4 1.18 min snp ratio 1.18 too small (less than 2.25)
5 1.15 min snp ratio 1.15 too small (less than 2.25)
6 0.90 min snp ratio 0.90 too small (less than 2.25)
8 0.97 min snp ratio 0.97 too small (less than 2.25)
no equivalent gene for [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G116A[0m nearest is [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m (1 snp, 0 indels):
CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCA[91mG[0mCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G116A[0m
CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAACCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
[91mnew[0m [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G116A[0m separated from [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m by 1 snp at: 116 (G --> A)
no equivalent gene for [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G270A[0m nearest is [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m (1 snp, 0 indels):
CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACG[91mG[0mCTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G270A[0m
CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGACTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
[91mnew[0m [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G270A[0m separated from [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m by 1 snp at: 270 (G --> A)
[95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m 21224 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
1 snp
[93m 19[0m 4.78 2.82 / 0.59 0 / 11461 23 / 3072 4 / 631 1 / 387 1 / 437 3 / 398 3 / 380 2 / 333 1 / 392 0 / 388 2 / 390
3 snps
236 1.98 8.32 / 4.21 0 / 11461 17 / 3072 4 / 631 17 / 387 40 / 437 48 / 398 55 / 380 27 / 333 29 / 392 27 / 388 43 / 390 32 / 454 43 / 357
[93m 84[0m 3.47 11. / 3.26 0 / 11461 0 / 3072 2 / 631 10 / 387 30 / 437 11 / 398 9 / 380 17 / 333 16 / 392 14 / 388 21 / 390 50 / 454 24 / 357
[93m 99[0m 2.68 6.65 / 2.48 0 / 11461 7 / 3072 0 / 631 8 / 387 28 / 437 19 / 398 11 / 380 19 / 333 36 / 392 18 / 388 30 / 390 31 / 454 29 / 357
3 snps
[93m216[0m 4.35 9.93 / 2.28 0 / 11461 20 / 3072 9 / 631 40 / 387 39 / 437 38 / 398 61 / 380 65 / 333 53 / 392 63 / 388 79 / 390 106 / 454 68 / 357
[93m 92[0m 4.66 9.95 / 2.13 0 / 11461 1 / 3072 2 / 631 9 / 387 17 / 437 12 / 398 15 / 380 12 / 333 34 / 392 17 / 388 39 / 390 25 / 454 19 / 357
[93m177[0m 3.11 3.25 / 1.05 0 / 11461 7 / 3072 2 / 631 12 / 387 14 / 437 25 / 398 11 / 380 18 / 333 18 / 392 18 / 388 28 / 390 22 / 454 19 / 357
4 snps
[93m185[0m 2.43 11. / 4.47 0 / 11461 5 / 3072 8 / 631 0 / 387 28 / 437 8 / 398 20 / 380 31 / 333 27 / 392 43 / 388 39 / 390 65 / 454 29 / 357 25 / 265
[93m281[0m 3.99 17. / 4.26 0 / 11461 17 / 3072 12 / 631 12 / 387 44 / 437 34 / 398 78 / 380 63 / 333 73 / 392 77 / 388 116 / 390 130 / 454 103 / 356 94 / 265
[93m 84[0m 2.54 10. / 4.11 0 / 11461 0 / 3072 2 / 631 10 / 387 30 / 437 11 / 398 9 / 380 17 / 333 16 / 392 14 / 388 21 / 390 50 / 454 24 / 357 12 / 265
140 1.35 5.56 / 4.11 0 / 11461 4 / 3072 19 / 631 2 / 387 26 / 437 6 / 398 8 / 380 2 / 333 9 / 392 4 / 388 12 / 389 4 / 454 0 / 357 4 / 265
4 snps
91 1.87 7.60 / 4.07 0 / 11461 9 / 3072 1 / 631 2 / 387 17 / 437 5 / 398 41 / 380 23 / 333 28 / 392 25 / 388 28 / 390 39 / 454 30 / 357 35 / 265
275 1.20 4.64 / 3.85 0 / 11461 28 / 3072 2 / 631 2 / 387 21 / 437 0 / 398 1 / 380 6 / 333 0 / 392 2 / 388 0 / 390 2 / 454 0 / 357 0 / 265
[93m236[0m 2.27 7.69 / 3.39 0 / 11461 17 / 3072 4 / 631 17 / 387 40 / 437 48 / 398 55 / 380 27 / 333 29 / 392 27 / 388 43 / 390 32 / 454 43 / 357 33 / 265
138 1.74 5.57 / 3.20 0 / 11461 17 / 3072 3 / 631 2 / 387 36 / 437 5 / 398 6 / 380 2 / 333 5 / 392 1 / 388 4 / 390 2 / 454 0 / 357 0 / 265
4 snps
215 1.01 2.62 / 2.59 0 / 11460 6 / 3072 1 / 631 7 / 387 26 / 437 7 / 398 6 / 380 10 / 333 4 / 392 11 / 388 11 / 390 13 / 454 10 / 357 13 / 265
131 1.08 2.32 / 2.15 0 / 11461 8 / 3072 2 / 631 5 / 387 25 / 437 9 / 398 8 / 380 6 / 333 7 / 392 5 / 388 8 / 390 10 / 454 16 / 357 13 / 265
225 1.57 2.86 / 1.82 0 / 11461 4 / 3072 0 / 631 2 / 387 25 / 437 5 / 398 5 / 380 6 / 333 5 / 392 4 / 388 3 / 390 2 / 454 3 / 357 6 / 265
[93m134[0m 2.43 4.29 / 1.77 0 / 11461 17 / 3072 4 / 631 5 / 387 22 / 437 5 / 398 7 / 380 2 / 333 7 / 392 5 / 388 6 / 390 2 / 454 1 / 357 4 / 265
5 snps
[93m166[0m 6.01 18. / 2.99 0 / 11461 2 / 3072 1 / 631 3 / 387 4 / 437 21 / 398 32 / 380 20 / 333 20 / 392 33 / 388 41 / 390 57 / 454 63 / 357 58 / 265 36 / 276
[93m253[0m 4.45 40. / 8.98 0 / 11461 13 / 3072 16 / 631 31 / 387 56 / 437 108 / 398 106 / 380 87 / 333 99 / 392 108 / 388 137 / 390 182 / 454 143 / 357 110 / 265 146 / 276
160 1.91 3.80 / 1.99 0 / 11461 34 / 3072 21 / 631 15 / 387 10 / 437 49 / 398 45 / 380 30 / 333 48 / 392 41 / 388 41 / 390 67 / 454 57 / 357 42 / 265 31 / 276
258 1.09 4.84 / 4.45 0 / 11461 11 / 3072 0 / 631 8 / 387 1 / 437 18 / 398 6 / 380 9 / 333 10 / 392 11 / 388 13 / 390 10 / 454 14 / 357 36 / 265 26 / 276
170 1.01 3.94 / 3.89 0 / 11461 15 / 3072 2 / 631 5 / 387 2 / 437 18 / 398 8 / 380 15 / 333 17 / 392 8 / 388 11 / 390 5 / 454 10 / 357 13 / 265 27 / 276
6 snps
[93m 91[0m 3.20 6.71 / 2.10 0 / 11461 9 / 3072 1 / 631 2 / 387 17 / 437 5 / 398 41 / 380 23 / 333 28 / 392 25 / 388 28 / 390 39 / 454 30 / 357 35 / 265 28 / 276 31 / 388
147 2.14 3.69 / 1.72 0 / 11461 3 / 3072 5 / 631 1 / 387 6 / 437 3 / 398 21 / 380 14 / 333 13 / 392 19 / 388 24 / 390 12 / 454 9 / 357 3 / 265 10 / 276 14 / 388
165 1.62 4.01 / 2.47 0 / 11461 12 / 3072 5 / 631 0 / 387 3 / 437 7 / 398 29 / 380 12 / 333 13 / 392 21 / 388 28 / 390 31 / 454 24 / 357 18 / 265 12 / 276 43 / 388
287 1.43 5.86 / 4.11 0 / 11461 19 / 3072 12 / 631 9 / 387 6 / 437 13 / 398 38 / 380 33 / 333 27 / 392 25 / 388 62 / 390 66 / 454 36 / 357 35 / 265 65 / 276 77 / 388
206 0.97 2.59 / 2.66 0 / 11461 7 / 3072 0 / 631 0 / 387 0 / 437 4 / 398 22 / 380 2 / 333 0 / 392 1 / 388 0 / 390 2 / 454 1 / 357 0 / 265 5 / 276 0 / 388
29 0.90 3.85 / 4.26 0 / 11461 2 / 3072 1 / 631 3 / 387 0 / 437 1 / 398 34 / 380 4 / 333 5 / 392 0 / 388 5 / 390 13 / 454 4 / 357 2 / 265 10 / 276 5 / 388
snps min ratio
1 4.78 candidate
3 1.98 min snp ratio 1.98 too small (less than 2.25)
3 3.11 positions 216 and 92 have inconsistent discontinuities
4 1.35 min snp ratio 1.35 too small (less than 2.25)
4 1.20 min snp ratio 1.20 too small (less than 2.25)
4 1.01 min snp ratio 1.01 too small (less than 2.25)
5 1.01 min snp ratio 1.01 too small (less than 2.25)
6 0.90 min snp ratio 0.90 too small (less than 2.25)
no equivalent gene for [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m nearest is [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m (1 snp, 0 indels):
CAGCTGCAGCTGCAGGAGT[91mC[0mGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m
CAGCTGCAGCTGCAGGAGTTGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m
[91mnew[0m [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m separated from [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m by 1 snp at: 19 (C --> T)
[95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m02[0m 1629 counts
[95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m 7564 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
1 snp
[93m260[0m 10. 89. / 8.67 0 / 3948 506 / 1427 55 / 180 20 / 83 34 / 142 24 / 115 23 / 112 28 / 121 5 / 117 32 / 113 31 / 125
1 snp
[93m114[0m 18. 2.72 / 0.15 0 / 3948 25 / 1426 3 / 180 1 / 83 1 / 142 1 / 115 1 / 112 2 / 121 1 / 117 1 / 113 0 / 125
snps min ratio
1 10. candidate
1 18. candidate
no equivalent gene for [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m nearest is [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m (1 snp, 0 indels):
CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGG[91mC[0mAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m
CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGTAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
[91mnew[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m separated from [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m by 1 snp at: 114 (C --> T)
no equivalent gene for [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+T260C[0m nearest is [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m (1 snp, 0 indels):
CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGC[91mT[0mGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+T260C[0m
CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
[91mnew[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+T260C[0m separated from [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m by 1 snp at: 260 (T --> C)
[95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m02[0m 5587 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
3 snps
[93m253[0m 3.77 12. / 3.31 0 / 2908 3 / 774 2 / 165 17 / 127 10 / 168 20 / 110 34 / 108 38 / 165 44 / 159 26 / 103 40 / 93 32 / 87 43 / 105
172 1.50 2.49 / 1.66 0 / 2905 6 / 774 3 / 165 12 / 127 9 / 168 7 / 110 17 / 107 32 / 165 24 / 157 22 / 103 23 / 92 16 / 87 21 / 105
166 1.47 4.81 / 3.27 0 / 2908 1 / 774 1 / 165 13 / 127 11 / 168 7 / 110 15 / 108 10 / 165 4 / 159 18 / 103 12 / 93 8 / 87 12 / 105
snps min ratio
3 1.47 min snp ratio 1.47 too small (less than 2.25)
[95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m 2937 counts
position ratio (one piece / two pieces) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
1 snp
[93m203[0m 6.69 158. / 24. 0 / 671 419 / 567 88 / 178 74 / 174 42 / 149 70 / 232 63 / 162 65 / 162 59 / 154 46 / 94 48 / 78
5 snps
205 1.94 4.97 / 2.55 0 / 671 0 / 567 0 / 178 3 / 174 5 / 149 28 / 232 15 / 162 16 / 162 9 / 154 14 / 94 21 / 78 10 / 66 2 / 48 5 / 77 3 / 39
214 1.58 5.82 / 3.68 0 / 671 3 / 567 6 / 178 9 / 174 5 / 149 36 / 232 42 / 162 24 / 162 22 / 154 22 / 94 13 / 78 22 / 66 3 / 48 23 / 77 13 / 39
34 1.51 6.57 / 4.35 0 / 671 0 / 567 0 / 178 0 / 174 0 / 149 20 / 232 9 / 162 7 / 162 42 / 154 2 / 94 9 / 78 1 / 66 0 / 48 1 / 77 2 / 39
175 1.48 5.25 / 3.56 0 / 671 1 / 567 7 / 178 2 / 174 13 / 149 45 / 232 16 / 162 13 / 162 12 / 154 14 / 94 11 / 78 4 / 66 4 / 48 18 / 77 4 / 39
179 1.36 3.96 / 2.91 0 / 671 2 / 567 6 / 178 14 / 174 0 / 149 14 / 232 19 / 162 19 / 162 10 / 154 5 / 94 10 / 78 9 / 66 7 / 48 17 / 77 9 / 39
8 snps
99 1.87 2.29 / 1.23 0 / 671 0 / 567 1 / 178 0 / 174 2 / 149 1 / 232 1 / 162 0 / 162 20 / 154 6 / 94 7 / 78 1 / 66 0 / 48 7 / 77 1 / 39 0 / 9 1 / 27 0 / 17
182 1.75 4.32 / 2.47 0 / 671 3 / 567 3 / 178 10 / 174 11 / 149 16 / 232 10 / 162 20 / 162 44 / 154 21 / 94 11 / 78 22 / 66 20 / 48 26 / 77 14 / 39 4 / 9 4 / 27 4 / 17
156 1.28 4.82 / 3.77 0 / 671 0 / 567 0 / 178 0 / 174 0 / 149 5 / 232 1 / 162 0 / 162 20 / 154 1 / 94 5 / 78 3 / 66 1 / 48 10 / 77 5 / 39 0 / 9 10 / 27 10 / 17
137 1.26 2.84 / 2.25 0 / 671 0 / 567 0 / 178 0 / 174 0 / 149 1 / 232 0 / 162 4 / 162 21 / 154 7 / 94 0 / 78 3 / 66 5 / 48 6 / 77 1 / 39 2 / 9 5 / 27 2 / 17
170 1.26 5.61 / 4.45 0 / 671 0 / 567 0 / 178 5 / 174 6 / 149 27 / 232 7 / 162 15 / 162 33 / 154 7 / 94 19 / 78 24 / 66 11 / 48 15 / 77 4 / 39 2 / 9 5 / 27 3 / 17
89 1.05 3.17 / 3.01 0 / 671 1 / 567 1 / 178 4 / 174 0 / 149 5 / 232 18 / 162 3 / 162 19 / 154 2 / 94 15 / 78 7 / 66 7 / 48 9 / 77 2 / 39 1 / 9 3 / 27 1 / 17
39 1.05 2.64 / 2.52 0 / 671 3 / 567 5 / 178 2 / 174 11 / 149 10 / 232 1 / 162 4 / 162 20 / 154 3 / 94 6 / 78 1 / 66 3 / 48 1 / 77 1 / 39 2 / 9 2 / 27 2 / 17
220 0.98 2.67 / 2.74 0 / 671 1 / 567 3 / 178 1 / 174 1 / 149 7 / 232 0 / 162 2 / 162 19 / 154 1 / 94 2 / 78 1 / 66 2 / 48 14 / 77 7 / 39 1 / 9 1 / 27 2 / 17
snps min ratio
1 6.69 candidate
5 1.36 min snp ratio 1.36 too small (less than 2.25)
8 0.98 min snp ratio 0.98 too small (less than 2.25)
no equivalent gene for [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03+C203T[0m nearest is [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m (1 snp, 0 indels):
GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCGGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGT[91mC[0mACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGA [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03+C203T[0m
GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCGGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTTACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGA [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m
[91mnew[0m [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03+C203T[0m separated from [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m by 1 snp at: 203 (C --> T)
found 11 new alleles: [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m10[0m [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02+G209T[0m [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m11[0m [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m01[0m [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m01[0m [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G116A[0m [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G270A[0m [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+T260C[0m [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03+C203T[0m
allele finding: 1323 fits in 36.0 sec
plotting allele finding (14.5 sec)
adding new allele to glfo:
template CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACGAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m
new CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATC[91mC[0mTTGGTA[91mT[0mAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGAC[91mA[0mAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m10[0m
adding new allele to glfo:
template CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGCTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m
new CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGCTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCAT[91mT[0mACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02+G209T[0m
[91mremoving[0m template gene [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m
adding new allele to glfo:
template CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGATTGCACGCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m
new C[91mG[0mGGTCACCTTGA[91mG[0mGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATG[91mT[0mGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGG[91mC[0mTTGCACGCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m11[0m
adding new allele to glfo:
template GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m
new GAGGTGCAGCTG[91mT[0mTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m01[0m
adding new allele to glfo:
template GAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGATCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGGTTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m
new GAGGTGCAGCTGGTGGAGTCTGG[91mG[0mGGAGGCTTG[91mG[0mTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGG[91mA[0mTTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGC[91mA[0mGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGC[91mT[0mGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m01[0m
adding new allele to glfo:
template CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
new CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCA[91mA[0mCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G116A[0m
adding new allele to glfo:
template CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
new CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACG[91mA[0mCTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G270A[0m
adding new allele to glfo:
template CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m
new CAGCTGCAGCTGCAGGAGT[91mT[0mGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m
adding new allele to glfo:
template CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
new CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGG[91mT[0mAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m
adding new allele to glfo:
template CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
new CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGC[91mC[0mGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+T260C[0m
adding new allele to glfo:
template GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCGGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGA [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m
new GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCGGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGT[91mT[0mACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGA [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03+C203T[0m
smith-waterman (writing parameters)
vsearch: 186583 / 238759 v annotations (52176 failed) with 49 v genes in 57.0 sec
running 15 procs for 181692 seqs
running 18 procs for 38817 seqs
info for 181137 / 238759 = 0.759 (57622 failed)
[91mwarning[0m smith-waterman step failed to find alignments for a large fraction of input sequences (see previous line) [91mnote:[0m maybe need to take reverse complement? (partis only searches in forward direction)
kept 88799 (0.372) unproductive
removed 4043 / 181137 = 0.02 duplicate sequences after trimming framework insertions (leaving 177094)
writing sw results to /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/sw-cache.yaml
plotting parameters in /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/plots/sw (16.3 sec)
writing parameters to /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/sw (1.7 sec)
water time: 808.5 (ig-sw 352.6 processing 143.4)
writing hmms (12.7 sec)
hmm
skipping matches from 2 genes without enough counts: [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m
prepare_for_hmm: (18.3 sec)
running 15 procs
calcd: vtb 177094 fwd 0
min-max time: 546.7 - 685.5 sec
read output
plotting parameters in /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/plots/hmm (14.8 sec)
writing parameters to /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/hmm (1.8 sec)
processed 177094 hmm output lines with 173650 sequences in 173650 events (3444 failures)
[91mwarning[0m skipped 3444 invalid events
infra time: 420.1
hmm step time: 1108.5
writing hmms (17.9 sec)
total time: 2895.3