Run ID: SRR13861251
Sample name:
Date: 03-04-2023 09:27:10
Number of reads: 296173
Percentage reads mapped: 14.82
Strain: lineage4.9
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 |
lineage4.9 | Euro-American (H37Rv-like) | T1 | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761135 | p.Leu443Phe | missense_variant | 0.18 | rifampicin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7427 | c.126G>C | synonymous_variant | 0.2 |
gyrA | 7442 | c.141G>C | synonymous_variant | 0.18 |
gyrA | 7451 | c.150C>G | synonymous_variant | 0.18 |
gyrA | 7457 | c.156T>C | synonymous_variant | 0.18 |
gyrA | 7466 | c.165G>A | synonymous_variant | 0.18 |
gyrA | 7469 | c.168C>T | synonymous_variant | 0.18 |
gyrA | 7472 | c.171T>C | synonymous_variant | 0.18 |
gyrA | 7475 | c.174A>C | synonymous_variant | 0.18 |
gyrA | 7480 | p.Phe60Tyr | missense_variant | 0.17 |
gyrA | 7484 | c.183T>C | synonymous_variant | 0.17 |
gyrA | 7487 | c.186C>G | synonymous_variant | 0.15 |
gyrA | 7490 | c.189C>T | synonymous_variant | 0.15 |
gyrA | 7523 | c.222C>G | synonymous_variant | 0.17 |
gyrA | 7532 | c.231T>C | synonymous_variant | 0.17 |
gyrA | 7541 | c.240C>G | synonymous_variant | 0.17 |
gyrA | 7697 | c.396C>G | synonymous_variant | 0.12 |
gyrA | 8711 | c.1410A>C | synonymous_variant | 0.25 |
gyrA | 8714 | c.1413A>G | synonymous_variant | 0.25 |
gyrA | 8717 | c.1416C>G | synonymous_variant | 0.25 |
gyrA | 8720 | c.1419G>A | synonymous_variant | 0.25 |
gyrA | 8729 | c.1428T>C | synonymous_variant | 0.22 |
gyrA | 8732 | c.1431G>C | synonymous_variant | 0.22 |
gyrA | 8747 | c.1446A>G | synonymous_variant | 0.25 |
gyrA | 8756 | c.1455A>G | synonymous_variant | 0.25 |
gyrA | 8762 | c.1461G>C | synonymous_variant | 0.25 |
gyrA | 8765 | p.Asp488Glu | missense_variant | 0.22 |
gyrA | 8767 | p.Arg489Lys | missense_variant | 0.22 |
gyrA | 8880 | p.Lys527Gln | missense_variant | 1.0 |
gyrA | 9305 | c.2004C>G | synonymous_variant | 0.18 |
fgd1 | 491094 | c.312C>G | synonymous_variant | 0.18 |
fgd1 | 491106 | c.324T>C | synonymous_variant | 0.18 |
fgd1 | 491121 | c.339A>G | synonymous_variant | 0.13 |
fgd1 | 491137 | p.Glu119Gln | missense_variant | 0.2 |
fgd1 | 491144 | p.Ala121Glu | missense_variant | 0.2 |
fgd1 | 491166 | c.384G>C | synonymous_variant | 0.15 |
fgd1 | 491181 | c.399T>C | synonymous_variant | 0.14 |
fgd1 | 491191 | p.Gly137Arg | missense_variant | 0.14 |
fgd1 | 491194 | c.412_414delCTAinsTTG | synonymous_variant | 0.13 |
fgd1 | 491202 | c.420G>C | synonymous_variant | 0.13 |
fgd1 | 491203 | p.Gln141Glu | missense_variant | 0.13 |
fgd1 | 491212 | p.Ser144Arg | missense_variant | 0.12 |
fgd1 | 491217 | c.435T>C | synonymous_variant | 0.12 |
fgd1 | 491241 | p.Asp153Glu | missense_variant | 0.16 |
fgd1 | 491259 | c.477T>C | synonymous_variant | 0.12 |
rpoB | 760475 | c.669A>G | synonymous_variant | 0.15 |
rpoB | 760481 | c.675G>C | synonymous_variant | 0.14 |
rpoB | 760514 | c.708C>T | synonymous_variant | 0.13 |
rpoB | 760522 | p.Ser239Asn | missense_variant | 0.14 |
rpoB | 760972 | p.Arg389Leu | missense_variant | 1.0 |
rpoB | 761150 | c.1344A>C | synonymous_variant | 0.18 |
rpoB | 761165 | c.1359G>C | synonymous_variant | 0.2 |
rpoB | 761168 | c.1362C>G | synonymous_variant | 0.2 |
rpoB | 761171 | c.1365C>T | synonymous_variant | 0.22 |
rpoB | 761180 | c.1374A>C | synonymous_variant | 0.22 |
rpoB | 761222 | c.1416G>C | synonymous_variant | 0.15 |
rpoB | 761249 | c.1443A>G | synonymous_variant | 0.15 |
rpoB | 761255 | c.1449T>G | synonymous_variant | 0.15 |
rpoB | 761261 | c.1455G>T | synonymous_variant | 0.18 |
rpoB | 761327 | c.1521A>G | synonymous_variant | 0.15 |
rpoC | 763158 | c.-212C>T | upstream_gene_variant | 0.15 |
rpoC | 763444 | c.75T>C | synonymous_variant | 0.12 |
rpoC | 763528 | c.159G>A | synonymous_variant | 0.12 |
rpoC | 763570 | c.201G>C | synonymous_variant | 0.13 |
rpoC | 763888 | c.519G>C | synonymous_variant | 0.14 |
rpoC | 764380 | c.1011G>C | synonymous_variant | 0.2 |
rpoC | 764381 | c.1012_1013delTCinsAG | synonymous_variant | 0.2 |
rpoC | 764387 | c.1018_1020delTTGinsCTC | synonymous_variant | 0.2 |
rpoC | 764405 | c.1036A>C | synonymous_variant | 0.17 |
rpoC | 764434 | c.1065A>G | synonymous_variant | 0.15 |
rpoC | 764446 | c.1077T>C | synonymous_variant | 0.15 |
rpoC | 764449 | c.1080G>C | synonymous_variant | 0.15 |
rpoC | 764455 | c.1086G>C | synonymous_variant | 0.14 |
rpoC | 764461 | c.1092A>G | synonymous_variant | 0.15 |
rpoC | 764497 | c.1128A>G | synonymous_variant | 0.18 |
rpoC | 764521 | c.1152T>C | synonymous_variant | 0.14 |
rpoC | 764530 | c.1161C>G | synonymous_variant | 0.15 |
rpoC | 764536 | c.1167G>C | synonymous_variant | 0.15 |
rpoC | 764539 | c.1170C>G | synonymous_variant | 0.15 |
rpoC | 764560 | c.1191T>C | synonymous_variant | 0.17 |
rpoC | 764566 | c.1197C>G | synonymous_variant | 0.18 |
rpoC | 764573 | c.1204_1206delCTTinsTTG | synonymous_variant | 0.18 |
rpoC | 764576 | c.1207_1208delTCinsAG | synonymous_variant | 0.18 |
rpoC | 764581 | c.1212T>C | synonymous_variant | 0.15 |
rpoC | 764626 | c.1257C>T | synonymous_variant | 0.13 |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.13 |
rpoC | 764764 | c.1395T>C | synonymous_variant | 0.12 |
rpoC | 764809 | c.1440C>T | synonymous_variant | 0.13 |
rpoC | 764812 | c.1443C>G | synonymous_variant | 0.13 |
rpoC | 764824 | c.1455T>C | synonymous_variant | 0.19 |
rpoC | 764830 | c.1461C>G | synonymous_variant | 0.15 |
rpoC | 764858 | c.1489T>C | synonymous_variant | 0.15 |
rpoC | 764872 | c.1503A>G | synonymous_variant | 0.17 |
rpoC | 764893 | c.1524T>C | synonymous_variant | 0.15 |
rpoC | 764911 | c.1542A>G | synonymous_variant | 0.27 |
rpoC | 764923 | c.1554A>G | synonymous_variant | 0.27 |
rpoC | 764932 | c.1563C>A | synonymous_variant | 0.27 |
rpoC | 764968 | c.1599T>C | synonymous_variant | 0.27 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.2 |
rpoC | 765007 | c.1638T>G | synonymous_variant | 0.2 |
rpoC | 765019 | c.1650A>G | synonymous_variant | 0.18 |
rpoC | 765022 | c.1653G>C | synonymous_variant | 0.2 |
rpoC | 765034 | c.1665T>C | synonymous_variant | 0.22 |
rpoC | 765040 | c.1671T>C | synonymous_variant | 0.22 |
rpoC | 765041 | c.1672T>C | synonymous_variant | 0.22 |
rpoC | 765047 | c.1678T>C | synonymous_variant | 0.22 |
rpoC | 765111 | p.Met581Lys | missense_variant | 1.0 |
rpoC | 765161 | p.Glu598Lys | missense_variant | 1.0 |
rpoC | 765331 | p.Ser654Arg | missense_variant | 0.14 |
rpoC | 765540 | p.Ala724Val | missense_variant | 1.0 |
rpoC | 766978 | c.3609C>G | synonymous_variant | 0.22 |
rpoC | 767068 | c.3699G>T | synonymous_variant | 0.89 |
rpoC | 767074 | c.3705T>C | synonymous_variant | 0.2 |
mmpR5 | 778439 | c.-551C>A | upstream_gene_variant | 1.0 |
rplC | 801357 | p.His183Gln | missense_variant | 1.0 |
fbiC | 1303911 | c.981G>C | synonymous_variant | 0.17 |
fbiC | 1303914 | c.984C>G | synonymous_variant | 0.17 |
fbiC | 1303920 | c.990C>G | synonymous_variant | 0.18 |
fbiC | 1303923 | c.993C>T | synonymous_variant | 0.18 |
fbiC | 1303929 | c.999G>C | synonymous_variant | 0.17 |
fbiC | 1303947 | c.1017T>C | synonymous_variant | 0.17 |
fbiC | 1303948 | p.Gly340Arg | missense_variant | 0.17 |
fbiC | 1303969 | p.Val347Ile | missense_variant | 0.17 |
fbiC | 1303995 | c.1065C>T | synonymous_variant | 0.14 |
fbiC | 1304001 | c.1071C>G | synonymous_variant | 0.14 |
fbiC | 1304008 | c.1078T>C | synonymous_variant | 0.15 |
fbiC | 1304229 | c.1301delC | frameshift_variant | 1.0 |
fbiC | 1304703 | c.1773C>G | synonymous_variant | 0.15 |
fbiC | 1304715 | c.1785G>C | synonymous_variant | 0.2 |
fbiC | 1304724 | c.1794A>G | synonymous_variant | 0.2 |
fbiC | 1304727 | c.1797A>G | synonymous_variant | 0.2 |
fbiC | 1304742 | c.1812T>C | synonymous_variant | 0.17 |
fbiC | 1304748 | c.1818T>C | synonymous_variant | 0.15 |
fbiC | 1304754 | c.1824G>A | synonymous_variant | 0.15 |
fbiC | 1304757 | c.1827A>G | synonymous_variant | 0.15 |
fbiC | 1304787 | c.1857T>C | synonymous_variant | 0.13 |
fbiC | 1304790 | c.1860C>G | synonymous_variant | 0.13 |
rrs | 1472288 | n.444delT | non_coding_transcript_exon_variant | 1.0 |
rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1473899 | n.242A>C | non_coding_transcript_exon_variant | 0.15 |
tlyA | 1917989 | p.Ala17Gly | missense_variant | 1.0 |
ndh | 2102525 | p.Phe173Tyr | missense_variant | 1.0 |
ndh | 2102538 | c.504_505insT | frameshift_variant | 1.0 |
Rv1979c | 2222978 | p.Ile63Phe | missense_variant | 1.0 |
Rv1979c | 2223052 | p.Glu38Val | missense_variant | 1.0 |
pncA | 2289415 | c.-174C>G | upstream_gene_variant | 1.0 |
kasA | 2518057 | c.-58A>C | upstream_gene_variant | 1.0 |
kasA | 2518799 | p.Pro229Ser | missense_variant | 0.88 |
eis | 2714983 | p.Ala117Glu | missense_variant | 1.0 |
folC | 2747394 | p.Ile69Val | missense_variant | 0.2 |
folC | 2747395 | c.204T>C | synonymous_variant | 0.2 |
folC | 2747401 | c.198G>C | synonymous_variant | 0.18 |
folC | 2747407 | c.192T>C | synonymous_variant | 0.18 |
folC | 2747411 | p.Ser63Ala | missense_variant | 0.18 |
folC | 2747416 | c.183A>G | synonymous_variant | 0.2 |
folC | 2747419 | c.180C>G | synonymous_variant | 0.22 |
folC | 2747430 | c.169C>T | synonymous_variant | 0.25 |
folC | 2747439 | p.Met54Leu | missense_variant | 0.17 |
folC | 2747442 | c.157T>C | synonymous_variant | 0.17 |
folC | 2747443 | c.156G>A | synonymous_variant | 0.17 |
thyX | 3067316 | c.630A>G | synonymous_variant | 0.2 |
thyX | 3067325 | c.621A>G | synonymous_variant | 0.2 |
thyX | 3067355 | c.591A>C | synonymous_variant | 0.18 |
thyX | 3067367 | c.579G>C | synonymous_variant | 0.22 |
thyX | 3067376 | c.570G>C | synonymous_variant | 0.18 |
thyX | 3067391 | c.555G>C | synonymous_variant | 0.21 |
thyX | 3067394 | c.552G>C | synonymous_variant | 0.21 |
thyX | 3067412 | c.534C>G | synonymous_variant | 0.21 |
thyX | 3067439 | c.507A>G | synonymous_variant | 0.2 |
thyX | 3067445 | c.501C>G | synonymous_variant | 0.19 |
thyX | 3067451 | c.495G>A | synonymous_variant | 0.18 |
thyX | 3067457 | c.489C>G | synonymous_variant | 0.19 |
fbiA | 3640404 | c.-139C>A | upstream_gene_variant | 1.0 |
fbiB | 3642056 | c.522C>G | synonymous_variant | 1.0 |
rpoA | 3877967 | p.Thr181Ser | missense_variant | 1.0 |
rpoA | 3877972 | c.535delG | frameshift_variant | 1.0 |
rpoA | 3878284 | p.Glu75Ala | missense_variant | 0.2 |
rpoA | 3878292 | c.216T>C | synonymous_variant | 0.18 |
rpoA | 3878298 | c.210A>G | synonymous_variant | 0.18 |
rpoA | 3878304 | c.204G>C | synonymous_variant | 0.2 |
rpoA | 3878313 | c.195G>C | synonymous_variant | 0.2 |
rpoA | 3878322 | c.186A>G | synonymous_variant | 0.22 |
rpoA | 3878331 | c.177A>G | synonymous_variant | 0.2 |
rpoA | 3878334 | c.174T>C | synonymous_variant | 0.22 |
rpoA | 3878337 | c.171T>C | synonymous_variant | 0.22 |
rpoA | 3878346 | c.162T>C | synonymous_variant | 0.22 |
clpC1 | 4038271 | p.Pro812Ala | missense_variant | 0.17 |
clpC1 | 4038272 | p.Gly811Ser | missense_variant | 0.17 |
clpC1 | 4038278 | c.2427T>C | synonymous_variant | 0.17 |
clpC1 | 4038293 | c.2412G>C | synonymous_variant | 0.18 |
clpC1 | 4038302 | c.2403C>G | synonymous_variant | 0.18 |
clpC1 | 4038308 | p.Val799Ile | missense_variant | 0.17 |
clpC1 | 4038317 | c.2388G>C | synonymous_variant | 0.15 |
clpC1 | 4038347 | c.2358G>C | synonymous_variant | 0.2 |
clpC1 | 4038356 | c.2349T>C | synonymous_variant | 0.22 |
clpC1 | 4038359 | c.2346A>G | synonymous_variant | 0.25 |
clpC1 | 4038368 | c.2337T>C | synonymous_variant | 0.3 |
clpC1 | 4038388 | c.2317T>C | synonymous_variant | 0.2 |
clpC1 | 4038398 | c.2307G>T | synonymous_variant | 0.18 |
clpC1 | 4038498 | p.Ser736Thr | missense_variant | 0.15 |
clpC1 | 4038790 | c.1915C>T | synonymous_variant | 0.15 |
clpC1 | 4038812 | c.1893T>C | synonymous_variant | 0.18 |
clpC1 | 4038815 | c.1890G>T | synonymous_variant | 0.17 |
clpC1 | 4038851 | c.1854G>A | synonymous_variant | 0.18 |
clpC1 | 4038878 | c.1827A>G | synonymous_variant | 0.22 |
clpC1 | 4038908 | c.1797C>G | synonymous_variant | 0.18 |
clpC1 | 4038914 | c.1791G>C | synonymous_variant | 0.25 |
clpC1 | 4038923 | c.1782A>G | synonymous_variant | 0.22 |
clpC1 | 4038932 | c.1773G>C | synonymous_variant | 0.22 |
clpC1 | 4039777 | c.927_928insG | frameshift_variant | 1.0 |
embB | 4247545 | p.Ser344Arg | missense_variant | 1.0 |
embB | 4248206 | p.Ser565Gly | missense_variant | 0.19 |
embB | 4248220 | c.1707A>G | synonymous_variant | 0.19 |
embB | 4248241 | c.1728C>T | synonymous_variant | 0.24 |
embB | 4248265 | c.1752C>T | synonymous_variant | 0.25 |
embB | 4248266 | c.1753C>T | synonymous_variant | 0.25 |
embB | 4248277 | c.1764G>C | synonymous_variant | 0.25 |
embB | 4248304 | c.1791G>T | synonymous_variant | 0.31 |
embB | 4248316 | c.1803C>G | synonymous_variant | 0.21 |
embB | 4248319 | c.1806A>G | synonymous_variant | 0.21 |
embB | 4248322 | c.1809G>C | synonymous_variant | 0.21 |
embB | 4248343 | c.1830G>C | synonymous_variant | 0.14 |
embB | 4248346 | c.1833G>C | synonymous_variant | 0.14 |
embB | 4248350 | c.1837T>C | synonymous_variant | 0.13 |
embB | 4248355 | c.1842A>G | synonymous_variant | 0.13 |
embB | 4248358 | c.1845C>G | synonymous_variant | 0.13 |
embB | 4248361 | c.1848A>G | synonymous_variant | 0.13 |
embB | 4248362 | p.Ser617Ala | missense_variant | 0.13 |
aftB | 4267580 | c.1257G>C | synonymous_variant | 0.12 |
aftB | 4268812 | p.Ser9Pro | missense_variant | 1.0 |