Run ID: ERR4829039
Sample name:
Date: 01-04-2023 19:14:44
Number of reads: 2391947
Percentage reads mapped: 81.39
Strain: lineage4.3.1
Drug-resistance: RR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.1 | Euro-American (LAM) | LAM9 | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761127 | p.Ser441Ala | missense_variant | 0.25 | rifampicin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 0.98 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.21 |
mshA | 576482 | p.Val379Leu | missense_variant | 0.13 |
rpoB | 761030 | c.1224G>C | synonymous_variant | 0.12 |
rpoB | 761037 | c.1231T>C | synonymous_variant | 0.18 |
rpoB | 761051 | c.1245G>C | synonymous_variant | 0.22 |
rpoB | 761054 | c.1248G>C | synonymous_variant | 0.23 |
rpoB | 761057 | c.1251G>C | synonymous_variant | 0.22 |
rpoB | 761060 | c.1254C>G | synonymous_variant | 0.22 |
rpoB | 761084 | c.1278C>A | synonymous_variant | 0.22 |
rpoB | 761088 | c.1282_1283delAGinsTC | synonymous_variant | 0.22 |
rpoB | 761096 | c.1290G>C | synonymous_variant | 0.22 |
rpoB | 761097 | c.1291_1293delAGCinsTCG | synonymous_variant | 0.22 |
rpoB | 761102 | c.1296A>G | synonymous_variant | 0.26 |
rpoB | 761123 | c.1317G>C | synonymous_variant | 0.25 |
rpoB | 761126 | c.1320G>C | synonymous_variant | 0.25 |
rpoB | 761132 | c.1326G>C | synonymous_variant | 0.25 |
rpoB | 761133 | c.1327T>C | synonymous_variant | 0.26 |
rpoB | 761150 | c.1344A>T | synonymous_variant | 0.24 |
rpoB | 761159 | c.1353G>C | synonymous_variant | 0.24 |
rpoB | 761165 | c.1359G>C | synonymous_variant | 0.23 |
rpoB | 761180 | c.1374A>G | synonymous_variant | 0.12 |
rpoB | 762143 | c.2337T>C | synonymous_variant | 0.11 |
rpoB | 762149 | c.2343G>C | synonymous_variant | 0.12 |
rpoB | 762156 | p.Val784Ile | missense_variant | 0.11 |
rpoB | 762167 | c.2361T>C | synonymous_variant | 0.12 |
rpoB | 762185 | c.2379G>C | synonymous_variant | 0.11 |
rpoC | 763053 | c.-317T>C | upstream_gene_variant | 0.12 |
rpoC | 763648 | c.279C>T | synonymous_variant | 0.11 |
rpoC | 763657 | p.Glu96Asp | missense_variant | 0.11 |
rpoC | 763660 | c.291T>G | synonymous_variant | 0.11 |
rpoC | 763666 | c.297G>C | synonymous_variant | 0.13 |
rpoC | 763675 | c.306C>G | synonymous_variant | 0.1 |
rpoC | 764485 | c.1116G>C | synonymous_variant | 0.14 |
rpoC | 764491 | c.1122G>T | synonymous_variant | 0.13 |
rpoC | 764497 | c.1128A>G | synonymous_variant | 0.14 |
rpoC | 764503 | c.1134G>T | synonymous_variant | 0.14 |
rpoC | 764509 | c.1140G>C | synonymous_variant | 0.14 |
rpoC | 764512 | c.1143G>C | synonymous_variant | 0.14 |
rpoC | 764521 | c.1152T>C | synonymous_variant | 0.16 |
rpoC | 764530 | c.1161C>T | synonymous_variant | 0.17 |
rpoC | 764536 | c.1167G>C | synonymous_variant | 0.17 |
rpoC | 764543 | p.Thr392Ala | missense_variant | 0.19 |
rpoC | 764548 | c.1179G>C | synonymous_variant | 0.19 |
rpoC | 764566 | c.1197C>G | synonymous_variant | 0.25 |
rpoC | 764573 | p.Leu402Ile | missense_variant | 0.26 |
rpoC | 764578 | c.1209C>G | synonymous_variant | 0.27 |
rpoC | 764581 | c.1212T>C | synonymous_variant | 0.26 |
rpoC | 764582 | p.Leu405Met | missense_variant | 0.25 |
rpoC | 764593 | c.1224C>T | synonymous_variant | 0.35 |
rpoC | 764602 | c.1233C>T | synonymous_variant | 0.37 |
rpoC | 764605 | c.1236G>T | synonymous_variant | 0.37 |
rpoC | 764611 | c.1242G>T | synonymous_variant | 0.34 |
rpoC | 764626 | c.1257C>T | synonymous_variant | 0.3 |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.28 |
rpoC | 764647 | c.1278C>T | synonymous_variant | 0.26 |
rpoC | 764650 | c.1281G>C | synonymous_variant | 0.25 |
rpoC | 764656 | c.1287C>T | synonymous_variant | 0.29 |
rpoC | 764662 | c.1293G>C | synonymous_variant | 0.29 |
rpoC | 764677 | c.1308C>G | synonymous_variant | 0.29 |
rpoC | 764678 | p.Lys437Gln | missense_variant | 0.28 |
rpoC | 764706 | p.Leu446Gln | missense_variant | 0.27 |
rpoC | 764713 | c.1344G>T | synonymous_variant | 0.24 |
rpoC | 764731 | c.1362G>C | synonymous_variant | 0.17 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472075 | n.230A>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472078 | n.233C>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472108 | n.263C>T | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472122 | n.277G>T | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472123 | n.278A>T | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472124 | n.279C>T | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.68 |
rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.64 |
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.65 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.59 |
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472285 | n.440A>G | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472400 | n.555C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472412 | n.567A>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472416 | n.571C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472422 | n.577T>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472427 | n.582T>G | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472435 | n.590T>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472436 | n.591G>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472437 | n.592T>G | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472438 | n.593T>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472448 | n.603T>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472449 | n.604C>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472450 | n.605A>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472451 | n.606C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472462 | n.617T>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472464 | n.619A>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472473 | n.628G>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472474 | n.629C>G | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472476 | n.631A>G | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472484 | n.639A>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472489 | n.644A>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472494 | n.649A>G | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472496 | n.651T>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472498 | n.653C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472513 | n.668T>C | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472549 | n.704G>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472581 | n.736A>C | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472584 | n.739A>T | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472647 | n.802C>T | non_coding_transcript_exon_variant | 0.59 |
rrs | 1472655 | n.810G>T | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472660 | n.815T>C | non_coding_transcript_exon_variant | 0.58 |
rrs | 1472686 | n.841G>T | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472687 | n.842A>T | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472690 | n.845C>T | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472692 | n.847T>C | non_coding_transcript_exon_variant | 0.51 |
rrs | 1472707 | n.862A>T | non_coding_transcript_exon_variant | 0.51 |
rrs | 1472714 | n.869A>G | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472790 | n.945T>C | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472825 | n.980G>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472954 | n.1109T>C | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472973 | n.1128A>G | non_coding_transcript_exon_variant | 0.55 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472992 | n.1147A>G | non_coding_transcript_exon_variant | 0.53 |
rrs | 1473005 | n.1160C>T | non_coding_transcript_exon_variant | 0.63 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.74 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.74 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.74 |
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.77 |
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.69 |
rrs | 1473081 | n.1236C>T | non_coding_transcript_exon_variant | 0.7 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.69 |
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.65 |
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 0.66 |
rrs | 1473101 | n.1256C>T | non_coding_transcript_exon_variant | 0.64 |
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.66 |
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 0.63 |
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.63 |
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.61 |
rrs | 1473123 | n.1278A>T | non_coding_transcript_exon_variant | 0.64 |
rrs | 1473130 | n.1285G>A | non_coding_transcript_exon_variant | 0.69 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.75 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.7 |
rrs | 1473172 | n.1327T>G | non_coding_transcript_exon_variant | 0.69 |
rrs | 1473173 | n.1328C>T | non_coding_transcript_exon_variant | 0.69 |
rrs | 1473221 | n.1376C>T | non_coding_transcript_exon_variant | 0.62 |
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.71 |
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.73 |
rrs | 1473276 | n.1431A>C | non_coding_transcript_exon_variant | 0.69 |
rrs | 1473277 | n.1432G>A | non_coding_transcript_exon_variant | 0.68 |
rrs | 1473300 | n.1455C>T | non_coding_transcript_exon_variant | 0.57 |
rrs | 1473301 | n.1456T>G | non_coding_transcript_exon_variant | 0.59 |
rrs | 1473316 | n.1471C>T | non_coding_transcript_exon_variant | 0.62 |
rrl | 1473384 | n.-274A>G | upstream_gene_variant | 0.21 |
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474516 | n.859C>A | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474537 | n.880G>A | non_coding_transcript_exon_variant | 0.1 |
rrl | 1474760 | n.1103A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474864 | n.1207C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475038 | n.1381G>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475715 | n.2058G>C | non_coding_transcript_exon_variant | 0.39 |
rrl | 1475751 | n.2094C>A | non_coding_transcript_exon_variant | 0.55 |
rrl | 1475756 | n.2099T>C | non_coding_transcript_exon_variant | 0.56 |
rrl | 1475765 | n.2108A>G | non_coding_transcript_exon_variant | 0.59 |
rrl | 1475767 | n.2110_2111insT | non_coding_transcript_exon_variant | 0.59 |
rrl | 1475777 | n.2120A>T | non_coding_transcript_exon_variant | 0.62 |
rrl | 1475883 | n.2226A>C | non_coding_transcript_exon_variant | 0.49 |
rrl | 1475884 | n.2227A>G | non_coding_transcript_exon_variant | 0.51 |
rrl | 1475896 | n.2239A>G | non_coding_transcript_exon_variant | 0.52 |
rrl | 1475897 | n.2240T>C | non_coding_transcript_exon_variant | 0.52 |
rrl | 1475898 | n.2241A>G | non_coding_transcript_exon_variant | 0.55 |
rrl | 1475899 | n.2242G>A | non_coding_transcript_exon_variant | 0.55 |
rrl | 1475906 | n.2249C>T | non_coding_transcript_exon_variant | 0.51 |
rrl | 1475916 | n.2259C>G | non_coding_transcript_exon_variant | 0.55 |
rrl | 1475937 | n.2280A>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.49 |
rrl | 1475945 | n.2288C>A | non_coding_transcript_exon_variant | 0.49 |
rrl | 1475952 | n.2295A>G | non_coding_transcript_exon_variant | 0.49 |
rrl | 1475970 | n.2313C>T | non_coding_transcript_exon_variant | 0.42 |
rrl | 1475975 | n.2318C>T | non_coding_transcript_exon_variant | 0.35 |
rrl | 1475977 | n.2320A>G | non_coding_transcript_exon_variant | 0.32 |
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475995 | n.2338G>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475997 | n.2340A>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1475998 | n.2341C>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476000 | n.2343G>A | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476001 | n.2344T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.7 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.76 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.78 |
rrl | 1476429 | n.2772A>T | non_coding_transcript_exon_variant | 0.77 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.8 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.7 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476513 | n.2856G>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476515 | n.2858C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476523 | n.2866T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476524 | n.2867C>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476539 | n.2882A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476542 | n.2885T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.19 |
rpsA | 1833721 | c.180A>G | synonymous_variant | 0.1 |
rpsA | 1833727 | c.186G>C | synonymous_variant | 0.1 |
rpsA | 1833742 | c.201A>G | synonymous_variant | 0.11 |
rpsA | 1834195 | c.654G>C | synonymous_variant | 0.14 |
rpsA | 1834228 | c.687C>T | synonymous_variant | 0.19 |
rpsA | 1834234 | c.693G>C | synonymous_variant | 0.17 |
rpsA | 1834240 | c.699T>C | synonymous_variant | 0.19 |
rpsA | 1834246 | c.705G>T | synonymous_variant | 0.22 |
rpsA | 1834249 | c.708T>C | synonymous_variant | 0.22 |
rpsA | 1834261 | c.720A>G | synonymous_variant | 0.22 |
rpsA | 1834264 | c.723G>C | synonymous_variant | 0.22 |
rpsA | 1834294 | c.753G>C | synonymous_variant | 0.32 |
rpsA | 1834298 | p.Gln253Glu | missense_variant | 0.32 |
rpsA | 1834306 | c.765T>C | synonymous_variant | 0.32 |
rpsA | 1834307 | p.Asp256Gln | missense_variant | 0.31 |
rpsA | 1834312 | c.771G>A | synonymous_variant | 0.3 |
rpsA | 1834327 | c.786G>T | synonymous_variant | 0.27 |
rpsA | 1834345 | c.804C>T | synonymous_variant | 0.23 |
rpsA | 1834348 | c.807T>C | synonymous_variant | 0.21 |
rpsA | 1834354 | c.813G>C | synonymous_variant | 0.19 |
rpsA | 1834357 | c.816T>C | synonymous_variant | 0.2 |
rpsA | 1834360 | c.819G>C | synonymous_variant | 0.18 |
rpsA | 1834361 | c.820T>C | synonymous_variant | 0.18 |
rpsA | 1834366 | c.825A>G | synonymous_variant | 0.18 |
rpsA | 1834375 | c.834G>C | synonymous_variant | 0.2 |
rpsA | 1834378 | c.837T>C | synonymous_variant | 0.21 |
rpsA | 1834387 | c.846C>T | synonymous_variant | 0.18 |
rpsA | 1834411 | c.870T>C | synonymous_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168412 | p.Phe734Cys | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.23 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246564 | p.Leu17Phe | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |