From: Choice of transcripts and software has a large effect on variant annotation
 | REF+ENS | REF | ENS | Match | REF match | ENS match | Overall match |
---|---|---|---|---|---|---|---|
 |  |  |  |  | rate (%) | rate (%) | rate (%) |
stopgain_SNV | 15,835 | 14,183 | 14,960 | 13,308 | 93.83 | 88.96 | 84.04 |
frameshift_insertion | 6,980 | 5,298 | 6,495 | 4,813 | 90.85 | 74.10 | 68.95 |
frameshift_deletion | 7,491 | 4,547 | 7,380 | 4,436 | 97.56 | 60.11 | 59.22 |
stoploss_SNV | 946 | 503 | 906 | 463 | 92.05 | 51.10 | 48.94 |
splicing | 47,878 | 14,154 | 45,839 | 12,115 | 85.59 | 26.43 | 25.30 |
frameshift_substitution | 1,960 | 195 | 1,947 | 182 | 93.33 | 9.35 | 9.29 |
nonsynonymous_SNV | 321,669 | 291,898 | 315,592 | 285,821 | 97.92 | 90.57 | 88.86 |
nonframeshift_insertion | 3,506 | 2,888 | 2,844 | 2,226 | 77.08 | 78.27 | 63.49 |
nonframeshift_deletion | 5,136 | 3,321 | 4,963 | 3,148 | 94.79 | 63.43 | 61.29 |
nonframeshift_substitution | 933 | 226 | 843 | 136 | 60.18 | 16.13 | 14.58 |
synonymous_SNV | 178,559 | 167,561 | 172,463 | 161,465 | 96.36 | 93.62 | 90.43 |
UTR3 | 724,802 | 574,255 | 622,441 | 471,894 | 82.17 | 75.81 | 65.11 |
UTR5 | 177,832 | 94,545 | 162,684 | 79,397 | 83.98 | 48.80 | 44.65 |
UTR5_UTR3 | 2,183 | 292 | 2,092 | 201 | 68.84 | 9.61 | 9.21 |
ncRNA_intronic | 8,992,009 | 2,113,428 | 8,244,441 | 1,365,860 | 64.63 | 16.57 | 15.19 |
ncRNA_exonic | 654,098 | 140,303 | 597,947 | 84,152 | 59.98 | 14.07 | 12.87 |
ncRNA_UTR3 | 53,379 | 10,712 | 47,133 | 4,466 | 41.69 | 9.48 | 8.37 |
ncRNA_UTR5 | 10,683 | 1,989 | 9,444 | 750 | 37.71 | 7.94 | 7.02 |
ncRNA_splicing | 13,931 | 1,051 | 13,562 | 682 | 64.89 | 5.03 | 4.90 |
ncRNA_UTR5_ncRNA_UTR3 | 107 | 1 | 106 | 0 | 0.00 | 0.00 | 0.00 |
intronic | 29,289,037 | 26,805,864 | 27,743,749 | 25,260,576 | 94.24 | 91.05 | 86.25 |
intergenic | 50,305,202 | 49,797,113 | 41,307,708 | 40,799,619 | 81.93 | 98.77 | 81.10 |
downstream | 991,811 | 474,684 | 840,376 | 323,249 | 68.10 | 38.46 | 32.59 |
upstream | 910,818 | 440,728 | 762,664 | 292,574 | 66.38 | 38.36 | 32.12 |
upstream_downstream | 53,608 | 15,621 | 47,293 | 9,306 | 59.57 | 19.68 | 17.36 |
unknown | 11,205 | 6,215 | 5,703 | 713 | 11.47 | 12.50 | 6.36 |
ALL LOF | 81,090 | 38,880 | 77,527 | 35,317 | 90.84 | 45.55 | 43.55 |
ALL LOF and MISSENSE | 412,334 | 337,213 | 401,769 | 326,648 | 96.87 | 81.30 | 79.22 |
ALL EXONIC | 590,893 | 504,774 | 574,232 | 488,113 | 96.70 | 85.00 | 82.61 |
ALL | 80,981,575 | 80,981,575 | 80,981,575 | 69,181,552 | 85.43 | 85.43 | 85.43 |