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view test-data/frameshift_deletions_check.tsv @ 1:029d90b0c4f6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit e702dcdbc7c3235ef3c4ee8998c7247d1af49465
| author | iuc |
|---|---|
| date | Fri, 14 Jul 2023 22:07:22 +0000 |
| parents | f079716f598c |
| children |
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ref_id start_position length VARIANT gene_region reads_all reads_fwd reads_rev deletions freq_del freq_del_fwd freq_del_rev deletions_fwd deletions_rev insertions freq_insert freq_insert_fwd freq_insert_rev insertions_fwd insertions_rev stops freq_stop freq_stop_fwd freq_stop_rev stops_fwd stops_rev matches_ref pos_critical_inserts pos_critical_dels homopolymeric ref_base cons_id variant_position_english variant_diagnosis NC_045512.2 5600 2 deletion ORF1ab 40 40 0 23 0.575 0.575 0 23 0 0 0.0 0.0 0 0 0 0 0 0 0 0 0 17 21101 8740,18800 1 T NC_045512.2 Gap of 2 nucleotide(s) found at refpos 5600 only fwd or rev reads available, deletion supported by the majority of them; homopolymeric; neighboring indels may restore reading frame NC_045512.2 5602 3 stopgain ORF1ab 40 40 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 40 1.0 1.0 0 40 0 40 . . 0 T NC_045512.2 Early Stopgain found at refpos 5602, aminoacid position 1779 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 5635 3 stopgain ORF1ab 40 40 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 40 1.0 1.0 0 40 0 40 . . 0 T NC_045512.2 Early Stopgain found at refpos 5635, aminoacid position 1790 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 5707 3 stopgain ORF1ab 63 39 24 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 63 1.0 1.0 1.0 39 24 63 . . 0 T NC_045512.2 Early Stopgain found at refpos 5707, aminoacid position 1814 stopgain supported by majority of fwd and rev reads NC_045512.2 5713 3 stopgain ORF1ab 72 39 33 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 72 1.0 1.0 1.0 39 33 72 . . 0 T NC_045512.2 Early Stopgain found at refpos 5713, aminoacid position 1816 stopgain supported by majority of fwd and rev reads NC_045512.2 5737 3 stopgain ORF1ab 79 39 40 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 79 1.0 1.0 1.0 39 40 79 . . 0 T NC_045512.2 Early Stopgain found at refpos 5737, aminoacid position 1824 stopgain supported by majority of fwd and rev reads NC_045512.2 5740 3 stopgain ORF1ab 79 39 40 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 79 1.0 1.0 1.0 39 40 79 . . 0 T NC_045512.2 Early Stopgain found at refpos 5740, aminoacid position 1825 stopgain supported by majority of fwd and rev reads NC_045512.2 5752 3 stopgain ORF1ab 79 39 40 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 79 1.0 1.0 1.0 39 40 79 . . 0 T NC_045512.2 Early Stopgain found at refpos 5752, aminoacid position 1829 stopgain supported by majority of fwd and rev reads NC_045512.2 5773 3 stopgain ORF1ab 78 38 40 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 78 1.0 1.0 1.0 38 40 78 . . 0 T NC_045512.2 Early Stopgain found at refpos 5773, aminoacid position 1836 stopgain supported by majority of fwd and rev reads NC_045512.2 5788 3 stopgain ORF1ab 74 34 40 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 74 1.0 1.0 1.0 34 40 74 . . 0 T NC_045512.2 Early Stopgain found at refpos 5788, aminoacid position 1841 stopgain supported by majority of fwd and rev reads NC_045512.2 5911 3 stopgain ORF1ab 45 5 40 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 45 1.0 1.0 1.0 5 40 45 . . 0 T NC_045512.2 Early Stopgain found at refpos 5911, aminoacid position 1882 stopgain supported by majority of fwd and rev reads NC_045512.2 6043 3 stopgain ORF1ab 10 5 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 10 1.0 1.0 1.0 5 5 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 6043, aminoacid position 1926 stopgain supported by majority of fwd and rev reads NC_045512.2 6049 3 stopgain ORF1ab 10 5 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 10 1.0 1.0 1.0 5 5 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 6049, aminoacid position 1928 stopgain supported by majority of fwd and rev reads NC_045512.2 6061 3 stopgain ORF1ab 10 5 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 10 1.0 1.0 1.0 5 5 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 6061, aminoacid position 1932 stopgain supported by majority of fwd and rev reads NC_045512.2 6064 3 stopgain ORF1ab 10 5 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 10 1.0 1.0 1.0 5 5 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 6064, aminoacid position 1933 stopgain supported by majority of fwd and rev reads NC_045512.2 6079 3 stopgain ORF1ab 10 5 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 10 1.0 1.0 1.0 5 5 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 6079, aminoacid position 1938 stopgain supported by majority of fwd and rev reads NC_045512.2 6082 3 stopgain ORF1ab 10 5 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 10 1.0 1.0 1.0 5 5 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 6082, aminoacid position 1939 stopgain supported by majority of fwd and rev reads NC_045512.2 6106 3 stopgain ORF1ab 10 5 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 10 1.0 1.0 1.0 5 5 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 6106, aminoacid position 1947 stopgain supported by majority of fwd and rev reads NC_045512.2 6202 3 stopgain ORF1ab 86 81 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 86 1.0 1.0 1.0 81 5 86 . . 0 T NC_045512.2 Early Stopgain found at refpos 6202, aminoacid position 1979 stopgain supported by majority of fwd and rev reads NC_045512.2 6214 3 stopgain ORF1ab 86 81 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 86 1.0 1.0 1.0 81 5 86 . . 0 T NC_045512.2 Early Stopgain found at refpos 6214, aminoacid position 1983 stopgain supported by majority of fwd and rev reads NC_045512.2 6226 3 stopgain ORF1ab 86 81 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 86 1.0 1.0 1.0 81 5 86 . . 0 T NC_045512.2 Early Stopgain found at refpos 6226, aminoacid position 1987 stopgain supported by majority of fwd and rev reads NC_045512.2 6247 3 stopgain ORF1ab 86 81 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 86 1.0 1.0 1.0 81 5 86 . . 0 T NC_045512.2 Early Stopgain found at refpos 6247, aminoacid position 1994 stopgain supported by majority of fwd and rev reads NC_045512.2 6259 3 stopgain ORF1ab 81 81 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 81 1.0 1.0 0 81 0 81 . . 0 T NC_045512.2 Early Stopgain found at refpos 6259, aminoacid position 1998 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 6262 3 stopgain ORF1ab 81 81 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 81 1.0 1.0 0 81 0 81 . . 0 T NC_045512.2 Early Stopgain found at refpos 6262, aminoacid position 1999 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 6274 3 stopgain ORF1ab 80 80 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 80 1.0 1.0 0 80 0 80 . . 0 T NC_045512.2 Early Stopgain found at refpos 6274, aminoacid position 2003 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 6322 3 stopgain ORF1ab 153 80 73 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 153 1.0 1.0 1.0 80 73 153 . . 0 T NC_045512.2 Early Stopgain found at refpos 6322, aminoacid position 2019 stopgain supported by majority of fwd and rev reads NC_045512.2 6340 3 stopgain ORF1ab 157 80 77 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 157 1.0 1.0 1.0 80 77 157 . . 0 T NC_045512.2 Early Stopgain found at refpos 6340, aminoacid position 2025 stopgain supported by majority of fwd and rev reads NC_045512.2 6376 3 stopgain ORF1ab 157 78 79 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 157 1.0 1.0 1.0 78 79 157 . . 0 T NC_045512.2 Early Stopgain found at refpos 6376, aminoacid position 2037 stopgain supported by majority of fwd and rev reads NC_045512.2 6409 3 stopgain ORF1ab 152 71 81 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 152 1.0 1.0 1.0 71 81 152 . . 0 T NC_045512.2 Early Stopgain found at refpos 6409, aminoacid position 2048 stopgain supported by majority of fwd and rev reads NC_045512.2 6451 3 stopgain ORF1ab 81 0 81 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 81 1.0 0 1.0 0 81 81 . . 0 T NC_045512.2 Early Stopgain found at refpos 6451, aminoacid position 2062 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 6457 3 stopgain ORF1ab 81 0 81 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 81 1.0 0 1.0 0 81 81 . . 0 T NC_045512.2 Early Stopgain found at refpos 6457, aminoacid position 2064 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 6496 3 stopgain ORF1ab 86 5 81 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 86 1.0 1.0 1.0 5 81 86 . . 0 T NC_045512.2 Early Stopgain found at refpos 6496, aminoacid position 2077 stopgain supported by majority of fwd and rev reads NC_045512.2 6508 3 stopgain ORF1ab 86 5 81 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 86 1.0 1.0 1.0 5 81 86 . . 0 T NC_045512.2 Early Stopgain found at refpos 6508, aminoacid position 2081 stopgain supported by majority of fwd and rev reads NC_045512.2 6511 3 stopgain ORF1ab 86 5 81 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 86 1.0 1.0 1.0 5 81 86 . . 0 T NC_045512.2 Early Stopgain found at refpos 6511, aminoacid position 2082 stopgain supported by majority of fwd and rev reads NC_045512.2 6655 3 stopgain ORF1ab 10 5 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 10 1.0 1.0 1.0 5 5 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 6655, aminoacid position 2130 stopgain supported by majority of fwd and rev reads NC_045512.2 6658 3 stopgain ORF1ab 10 5 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 10 1.0 1.0 1.0 5 5 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 6658, aminoacid position 2131 stopgain supported by majority of fwd and rev reads NC_045512.2 6682 3 stopgain ORF1ab 10 5 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 10 1.0 1.0 1.0 5 5 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 6682, aminoacid position 2139 stopgain supported by majority of fwd and rev reads NC_045512.2 6691 3 stopgain ORF1ab 10 5 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 10 1.0 1.0 1.0 5 5 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 6691, aminoacid position 2142 stopgain supported by majority of fwd and rev reads NC_045512.2 7342 3 stopgain ORF1ab 173 169 4 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 173 1.0 1.0 1.0 169 4 173 . . 0 T NC_045512.2 Early Stopgain found at refpos 7342, aminoacid position 2359 stopgain supported by majority of fwd and rev reads NC_045512.2 7345 3 stopgain ORF1ab 173 169 4 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 173 1.0 1.0 1.0 169 4 173 . . 0 T NC_045512.2 Early Stopgain found at refpos 7345, aminoacid position 2360 stopgain supported by majority of fwd and rev reads NC_045512.2 7372 3 stopgain ORF1ab 173 169 4 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 173 1.0 1.0 1.0 169 4 173 . . 0 T NC_045512.2 Early Stopgain found at refpos 7372, aminoacid position 2369 stopgain supported by majority of fwd and rev reads NC_045512.2 7408 3 stopgain ORF1ab 168 168 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 168 1.0 1.0 0 168 0 168 . . 0 T NC_045512.2 Early Stopgain found at refpos 7408, aminoacid position 2381 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 7477 3 stopgain ORF1ab 330 167 163 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 330 1.0 1.0 1.0 167 163 330 . . 0 T NC_045512.2 Early Stopgain found at refpos 7477, aminoacid position 2404 stopgain supported by majority of fwd and rev reads NC_045512.2 7510 3 stopgain ORF1ab 334 166 168 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 334 1.0 1.0 1.0 166 168 334 . . 0 T NC_045512.2 Early Stopgain found at refpos 7510, aminoacid position 2415 stopgain supported by majority of fwd and rev reads NC_045512.2 7513 3 stopgain ORF1ab 333 165 168 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 333 1.0 1.0 1.0 165 168 333 . . 0 T NC_045512.2 Early Stopgain found at refpos 7513, aminoacid position 2416 stopgain supported by majority of fwd and rev reads NC_045512.2 7546 3 stopgain ORF1ab 309 141 168 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 309 1.0 1.0 1.0 141 168 309 . . 0 T NC_045512.2 Early Stopgain found at refpos 7546, aminoacid position 2427 stopgain supported by majority of fwd and rev reads NC_045512.2 7555 3 stopgain ORF1ab 289 121 168 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 289 1.0 1.0 1.0 121 168 289 . . 0 T NC_045512.2 Early Stopgain found at refpos 7555, aminoacid position 2430 stopgain supported by majority of fwd and rev reads NC_045512.2 7579 3 stopgain ORF1ab 169 0 169 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 169 1.0 0 1.0 0 169 169 . . 0 T NC_045512.2 Early Stopgain found at refpos 7579, aminoacid position 2438 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 7588 3 stopgain ORF1ab 169 0 169 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 169 1.0 0 1.0 0 169 169 . . 0 T NC_045512.2 Early Stopgain found at refpos 7588, aminoacid position 2441 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 7624 3 stopgain ORF1ab 170 0 170 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 170 1.0 0 1.0 0 170 170 . . 0 T NC_045512.2 Early Stopgain found at refpos 7624, aminoacid position 2453 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 7630 3 stopgain ORF1ab 170 0 170 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 170 1.0 0 1.0 0 170 170 . . 0 T NC_045512.2 Early Stopgain found at refpos 7630, aminoacid position 2455 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 7648 3 stopgain ORF1ab 170 0 170 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 170 1.0 0 1.0 0 170 170 . . 0 T NC_045512.2 Early Stopgain found at refpos 7648, aminoacid position 2461 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 7660 3 stopgain ORF1ab 176 6 170 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 176 1.0 1.0 1.0 6 170 176 . . 0 T NC_045512.2 Early Stopgain found at refpos 7660, aminoacid position 2465 stopgain supported by majority of fwd and rev reads NC_045512.2 7663 3 stopgain ORF1ab 176 6 170 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 173 0.9829545454545454 1.0 0.9823529411764705 6 167 173 . . 0 T NC_045512.2 Early Stopgain found at refpos 7663, aminoacid position 2466 stopgain supported by majority of fwd and rev reads NC_045512.2 7666 3 stopgain ORF1ab 176 6 170 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 176 1.0 1.0 1.0 6 170 176 . . 0 T NC_045512.2 Early Stopgain found at refpos 7666, aminoacid position 2467 stopgain supported by majority of fwd and rev reads NC_045512.2 7780 3 stopgain ORF1ab 11 6 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 11 1.0 1.0 1.0 6 5 11 . . 0 T NC_045512.2 Early Stopgain found at refpos 7780, aminoacid position 2505 stopgain supported by majority of fwd and rev reads NC_045512.2 7783 3 stopgain ORF1ab 11 6 5 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 11 1.0 1.0 1.0 6 5 11 . . 0 T NC_045512.2 Early Stopgain found at refpos 7783, aminoacid position 2506 stopgain supported by majority of fwd and rev reads NC_045512.2 7804 3 stopgain ORF1ab 12 6 6 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 12 1.0 1.0 1.0 6 6 12 . . 0 T NC_045512.2 Early Stopgain found at refpos 7804, aminoacid position 2513 stopgain supported by majority of fwd and rev reads NC_045512.2 7831 3 stopgain ORF1ab 12 6 6 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 12 1.0 1.0 1.0 6 6 12 . . 0 T NC_045512.2 Early Stopgain found at refpos 7831, aminoacid position 2522 stopgain supported by majority of fwd and rev reads NC_045512.2 7852 3 stopgain ORF1ab 12 6 6 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 12 1.0 1.0 1.0 6 6 12 . . 0 T NC_045512.2 Early Stopgain found at refpos 7852, aminoacid position 2529 stopgain supported by majority of fwd and rev reads NC_045512.2 7855 3 stopgain ORF1ab 12 6 6 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 12 1.0 1.0 1.0 6 6 12 . . 0 T NC_045512.2 Early Stopgain found at refpos 7855, aminoacid position 2530 stopgain supported by majority of fwd and rev reads NC_045512.2 7861 3 stopgain ORF1ab 11 5 6 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 11 1.0 1.0 1.0 5 6 11 . . 0 T NC_045512.2 Early Stopgain found at refpos 7861, aminoacid position 2532 stopgain supported by majority of fwd and rev reads NC_045512.2 7999 3 stopgain ORF1ab 23 23 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 23 1.0 1.0 0 23 0 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 7999, aminoacid position 2578 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8008 3 stopgain ORF1ab 23 23 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 23 1.0 1.0 0 23 0 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8008, aminoacid position 2581 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8011 3 stopgain ORF1ab 23 23 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 23 1.0 1.0 0 23 0 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8011, aminoacid position 2582 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8029 3 stopgain ORF1ab 23 23 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 23 1.0 1.0 0 23 0 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8029, aminoacid position 2588 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8038 3 stopgain ORF1ab 23 23 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 23 1.0 1.0 0 23 0 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8038, aminoacid position 2591 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8050 3 stopgain ORF1ab 23 23 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 23 1.0 1.0 0 23 0 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8050, aminoacid position 2595 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8071 3 stopgain ORF1ab 23 23 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 23 1.0 1.0 0 23 0 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8071, aminoacid position 2602 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8119 3 stopgain ORF1ab 46 23 23 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 46 1.0 1.0 1.0 23 23 46 . . 0 T NC_045512.2 Early Stopgain found at refpos 8119, aminoacid position 2618 stopgain supported by majority of fwd and rev reads NC_045512.2 8191 3 stopgain ORF1ab 42 19 23 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 42 1.0 1.0 1.0 19 23 42 . . 0 T NC_045512.2 Early Stopgain found at refpos 8191, aminoacid position 2642 stopgain supported by majority of fwd and rev reads NC_045512.2 8209 3 stopgain ORF1ab 23 0 23 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 23 1.0 0 1.0 0 23 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8209, aminoacid position 2648 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8221 3 stopgain ORF1ab 23 0 23 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 23 1.0 0 1.0 0 23 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8221, aminoacid position 2652 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8230 3 stopgain ORF1ab 23 0 23 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 23 1.0 0 1.0 0 23 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8230, aminoacid position 2655 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8248 3 stopgain ORF1ab 23 0 23 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 23 1.0 0 1.0 0 23 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8248, aminoacid position 2661 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8269 3 stopgain ORF1ab 23 0 23 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 23 1.0 0 1.0 0 23 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8269, aminoacid position 2668 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8275 3 stopgain ORF1ab 23 0 23 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 23 1.0 0 1.0 0 23 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8275, aminoacid position 2670 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8278 3 stopgain ORF1ab 23 0 23 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 23 1.0 0 1.0 0 23 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8278, aminoacid position 2671 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8296 3 stopgain ORF1ab 23 0 23 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 23 1.0 0 1.0 0 23 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8296, aminoacid position 2677 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8305 3 stopgain ORF1ab 23 0 23 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 23 1.0 0 1.0 0 23 23 . . 0 T NC_045512.2 Early Stopgain found at refpos 8305, aminoacid position 2680 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8656 3 stopgain ORF1ab 10 10 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 10 1.0 1.0 0 10 0 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 8656, aminoacid position 2797 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8665 3 stopgain ORF1ab 10 10 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 10 1.0 1.0 0 10 0 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 8665, aminoacid position 2800 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8677 3 stopgain ORF1ab 10 10 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 10 1.0 1.0 0 10 0 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 8677, aminoacid position 2804 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8701 3 stopgain ORF1ab 10 10 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 10 1.0 1.0 0 10 0 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 8701, aminoacid position 2812 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8719 3 stopgain ORF1ab 10 10 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 10 1.0 1.0 0 10 0 10 . . 0 T NC_045512.2 Early Stopgain found at refpos 8719, aminoacid position 2818 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 8740 1 deletion ORF1ab 20 10 10 10 0.5 0.5 0.5 5 5 0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 10 21101 5600,5601,18800 1 T NC_045512.2 Gap of 1 nucleotide(s) found at refpos 8740 deletion supported by minority of fwd or rev reads 5%-50%; homopolymeric; neighboring indels may restore reading frame NC_045512.2 9791 3 stopgain ORF1ab 23 0 23 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 23 1.0 0 1.0 0 23 0 . . 0 G NC_045512.2 Early Stopgain found at refpos 9791, aminoacid position 3175, with 1 mismatches only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 18800 1 deletion ORF1ab 111 54 57 66 0.5945945945945946 0.5925925925925926 0.5964912280701754 32 34 0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 45 21101 5600,5601,8740 1 A NC_045512.2 Gap of 1 nucleotide(s) found at refpos 18800 deletion supported by majority of fwd and rev reads; homopolymeric; neighboring indels may restore reading frame NC_045512.2 18845 3 stopgain ORF1ab 104 47 57 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 104 1.0 1.0 1.0 47 57 104 . . 0 T NC_045512.2 Early Stopgain found at refpos 18845, aminoacid position 6193 stopgain supported by majority of fwd and rev reads NC_045512.2 18866 3 stopgain ORF1ab 57 0 57 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 57 1.0 0 1.0 0 57 57 . . 0 T NC_045512.2 Early Stopgain found at refpos 18866, aminoacid position 6200 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 18878 3 stopgain ORF1ab 57 0 57 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 57 1.0 0 1.0 0 57 57 . . 0 T NC_045512.2 Early Stopgain found at refpos 18878, aminoacid position 6204 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 18932 3 stopgain ORF1ab 65 8 57 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 65 1.0 1.0 1.0 8 57 65 . . 0 T NC_045512.2 Early Stopgain found at refpos 18932, aminoacid position 6222 stopgain supported by majority of fwd and rev reads NC_045512.2 18947 3 stopgain ORF1ab 65 8 57 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 65 1.0 1.0 1.0 8 57 65 . . 0 T NC_045512.2 Early Stopgain found at refpos 18947, aminoacid position 6227 stopgain supported by majority of fwd and rev reads NC_045512.2 19076 3 stopgain ORF1ab 16 8 8 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 16 1.0 1.0 1.0 8 8 16 . . 0 T NC_045512.2 Early Stopgain found at refpos 19076, aminoacid position 6270 stopgain supported by majority of fwd and rev reads NC_045512.2 19127 3 stopgain ORF1ab 16 8 8 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 16 1.0 1.0 1.0 8 8 16 . . 0 T NC_045512.2 Early Stopgain found at refpos 19127, aminoacid position 6287 stopgain supported by majority of fwd and rev reads NC_045512.2 19301 3 stopgain ORF1ab 104 104 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 104 1.0 1.0 0 104 0 104 . . 0 T NC_045512.2 Early Stopgain found at refpos 19301, aminoacid position 6345 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 19355 3 stopgain ORF1ab 104 104 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 104 1.0 1.0 0 104 0 104 . . 0 T NC_045512.2 Early Stopgain found at refpos 19355, aminoacid position 6363 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 19415 3 stopgain ORF1ab 201 101 100 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 201 1.0 1.0 1.0 101 100 201 . . 0 T NC_045512.2 Early Stopgain found at refpos 19415, aminoacid position 6383 stopgain supported by majority of fwd and rev reads NC_045512.2 19427 3 stopgain ORF1ab 200 100 100 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 200 1.0 1.0 1.0 100 100 200 . . 0 T NC_045512.2 Early Stopgain found at refpos 19427, aminoacid position 6387 stopgain supported by majority of fwd and rev reads NC_045512.2 19442 3 stopgain ORF1ab 197 96 101 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 197 1.0 1.0 1.0 96 101 197 . . 0 T NC_045512.2 Early Stopgain found at refpos 19442, aminoacid position 6392 stopgain supported by majority of fwd and rev reads NC_045512.2 19460 3 stopgain ORF1ab 108 7 101 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 108 1.0 1.0 1.0 7 101 108 . . 0 T NC_045512.2 Early Stopgain found at refpos 19460, aminoacid position 6398 stopgain supported by majority of fwd and rev reads NC_045512.2 19475 3 stopgain ORF1ab 103 0 103 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 103 1.0 0 1.0 0 103 103 . . 0 T NC_045512.2 Early Stopgain found at refpos 19475, aminoacid position 6403 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 19538 3 stopgain ORF1ab 103 0 103 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 103 1.0 0 1.0 0 103 103 . . 0 T NC_045512.2 Early Stopgain found at refpos 19538, aminoacid position 6424 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 19541 3 stopgain ORF1ab 103 0 103 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 103 1.0 0 1.0 0 103 103 . . 0 T NC_045512.2 Early Stopgain found at refpos 19541, aminoacid position 6425 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 19625 3 stopgain ORF1ab 39 39 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 39 1.0 1.0 0 39 0 39 . . 0 T NC_045512.2 Early Stopgain found at refpos 19625, aminoacid position 6453 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 19649 3 stopgain ORF1ab 40 39 1 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 40 1.0 1.0 1.0 39 1 40 . . 0 T NC_045512.2 Early Stopgain found at refpos 19649, aminoacid position 6461 stopgain supported by majority of fwd and rev reads NC_045512.2 19739 3 stopgain ORF1ab 78 39 39 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 78 1.0 1.0 1.0 39 39 78 . . 0 T NC_045512.2 Early Stopgain found at refpos 19739, aminoacid position 6491 stopgain supported by majority of fwd and rev reads NC_045512.2 19778 3 stopgain ORF1ab 77 38 39 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 77 1.0 1.0 1.0 38 39 77 . . 0 T NC_045512.2 Early Stopgain found at refpos 19778, aminoacid position 6504 stopgain supported by majority of fwd and rev reads NC_045512.2 19826 3 stopgain ORF1ab 39 0 39 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 39 1.0 0 1.0 0 39 39 . . 0 T NC_045512.2 Early Stopgain found at refpos 19826, aminoacid position 6520 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 19871 3 stopgain ORF1ab 108 69 39 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 108 1.0 1.0 1.0 69 39 108 . . 0 T NC_045512.2 Early Stopgain found at refpos 19871, aminoacid position 6535 stopgain supported by majority of fwd and rev reads NC_045512.2 19931 3 stopgain ORF1ab 69 69 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 69 1.0 1.0 0 69 0 69 . . 0 T NC_045512.2 Early Stopgain found at refpos 19931, aminoacid position 6555 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 19940 3 stopgain ORF1ab 69 69 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 68 0.9855072463768116 0.9855072463768116 0 68 0 68 . . 0 T NC_045512.2 Early Stopgain found at refpos 19940, aminoacid position 6558 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 20012 3 stopgain ORF1ab 131 69 62 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 131 1.0 1.0 1.0 69 62 131 . . 0 T NC_045512.2 Early Stopgain found at refpos 20012, aminoacid position 6582 stopgain supported by majority of fwd and rev reads NC_045512.2 20084 3 stopgain ORF1ab 133 64 69 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 133 1.0 1.0 1.0 64 69 133 . . 0 T NC_045512.2 Early Stopgain found at refpos 20084, aminoacid position 6606 stopgain supported by majority of fwd and rev reads NC_045512.2 20120 3 stopgain ORF1ab 69 0 69 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 69 1.0 0 1.0 0 69 69 . . 0 T NC_045512.2 Early Stopgain found at refpos 20120, aminoacid position 6618 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 20135 3 stopgain ORF1ab 69 0 69 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 69 1.0 0 1.0 0 69 69 . . 0 T NC_045512.2 Early Stopgain found at refpos 20135, aminoacid position 6623 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 20534 3 stopgain ORF1ab 251 251 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 251 1.0 1.0 0 251 0 251 . . 0 T NC_045512.2 Early Stopgain found at refpos 20534, aminoacid position 6756 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 20537 3 stopgain ORF1ab 251 251 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 251 1.0 1.0 0 251 0 251 . . 0 T NC_045512.2 Early Stopgain found at refpos 20537, aminoacid position 6757 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 20558 3 stopgain ORF1ab 250 250 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 250 1.0 1.0 0 250 0 250 . . 0 T NC_045512.2 Early Stopgain found at refpos 20558, aminoacid position 6764 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 20579 3 stopgain ORF1ab 250 250 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 250 1.0 1.0 0 250 0 250 . . 0 T NC_045512.2 Early Stopgain found at refpos 20579, aminoacid position 6771 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 20633 3 stopgain ORF1ab 250 249 1 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 250 1.0 1.0 1.0 249 1 250 . . 0 T NC_045512.2 Early Stopgain found at refpos 20633, aminoacid position 6789 stopgain supported by majority of fwd and rev reads NC_045512.2 20723 3 stopgain ORF1ab 442 194 248 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 442 1.0 1.0 1.0 194 248 442 . . 0 T NC_045512.2 Early Stopgain found at refpos 20723, aminoacid position 6819 stopgain supported by majority of fwd and rev reads NC_045512.2 20777 3 stopgain ORF1ab 250 0 250 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 250 1.0 0 1.0 0 250 250 . . 0 T NC_045512.2 Early Stopgain found at refpos 20777, aminoacid position 6837 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 20780 3 stopgain ORF1ab 250 0 250 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 250 1.0 0 1.0 0 250 250 . . 0 T NC_045512.2 Early Stopgain found at refpos 20780, aminoacid position 6838 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 20783 3 stopgain ORF1ab 250 0 250 0 0.0 0 0.0 0 0 0 0.0 0 0.0 0 0 250 1.0 0 1.0 0 250 250 . . 0 T NC_045512.2 Early Stopgain found at refpos 20783, aminoacid position 6839 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 20819 3 stopgain ORF1ab 275 24 251 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 275 1.0 1.0 1.0 24 251 275 . . 0 T NC_045512.2 Early Stopgain found at refpos 20819, aminoacid position 6851 stopgain supported by majority of fwd and rev reads NC_045512.2 20828 3 stopgain ORF1ab 275 24 251 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 274 0.9963636363636363 1.0 0.9960159362549801 24 250 274 . . 0 T NC_045512.2 Early Stopgain found at refpos 20828, aminoacid position 6854 stopgain supported by majority of fwd and rev reads NC_045512.2 20834 3 stopgain ORF1ab 275 24 251 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 275 1.0 1.0 1.0 24 251 275 . . 0 T NC_045512.2 Early Stopgain found at refpos 20834, aminoacid position 6856 stopgain supported by majority of fwd and rev reads NC_045512.2 20852 3 stopgain ORF1ab 275 24 251 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 275 1.0 1.0 1.0 24 251 275 . . 0 T NC_045512.2 Early Stopgain found at refpos 20852, aminoacid position 6862 stopgain supported by majority of fwd and rev reads NC_045512.2 20912 3 stopgain ORF1ab 24 24 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 24 1.0 1.0 0 24 0 24 . . 0 T NC_045512.2 Early Stopgain found at refpos 20912, aminoacid position 6882 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 20990 3 stopgain ORF1ab 48 24 24 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 48 1.0 1.0 1.0 24 24 48 . . 0 T NC_045512.2 Early Stopgain found at refpos 20990, aminoacid position 6908 stopgain supported by majority of fwd and rev reads NC_045512.2 21140 3 stopgain ORF1ab 41 17 24 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 41 1.0 1.0 1.0 17 24 41 . . 0 T NC_045512.2 Early Stopgain found at refpos 21140, aminoacid position 6958 stopgain supported by majority of fwd and rev reads NC_045512.2 21164 3 stopgain ORF1ab 17 17 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 17 1.0 1.0 0 17 0 17 . . 0 T NC_045512.2 Early Stopgain found at refpos 21164, aminoacid position 6966 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 21170 3 stopgain ORF1ab 17 17 0 0 0.0 0.0 0 0 0 0 0.0 0.0 0 0 0 17 1.0 1.0 0 17 0 17 . . 0 T NC_045512.2 Early Stopgain found at refpos 21170, aminoacid position 6968 only fwd or rev reads available, stopgain supported by the majority of them NC_045512.2 21248 3 stopgain ORF1ab 34 17 17 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 34 1.0 1.0 1.0 17 17 34 . . 0 T NC_045512.2 Early Stopgain found at refpos 21248, aminoacid position 6994 stopgain supported by majority of fwd and rev reads NC_045512.2 21275 3 stopgain ORF1ab 34 17 17 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 34 1.0 1.0 1.0 17 17 34 . . 0 T NC_045512.2 Early Stopgain found at refpos 21275, aminoacid position 7003 stopgain supported by majority of fwd and rev reads NC_045512.2 21314 3 stopgain ORF1ab 31 14 17 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 31 1.0 1.0 1.0 14 17 31 . . 0 T NC_045512.2 Early Stopgain found at refpos 21314, aminoacid position 7016 stopgain supported by majority of fwd and rev reads NC_045512.2 21398 3 stopgain ORF1ab 21 4 17 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 21 1.0 1.0 1.0 4 17 21 . . 0 T NC_045512.2 Early Stopgain found at refpos 21398, aminoacid position 7044 stopgain supported by majority of fwd and rev reads NC_045512.2 21419 3 stopgain ORF1ab 21 4 17 0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0 0 21 1.0 1.0 1.0 4 17 21 . . 0 T NC_045512.2 Early Stopgain found at refpos 21419, aminoacid position 7051 stopgain supported by majority of fwd and rev reads