Run ID: SRR13591342
Sample name:
Date: 03-04-2023 09:03:59
Number of reads: 1497232
Percentage reads mapped: 84.66
Strain: lineage4.1.1.3
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.1 | Euro-American | T;X;H | None | 0.97 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 0.99 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.99 | isoniazid, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 6919 | c.-383T>C | upstream_gene_variant | 0.18 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8516 | c.1215T>C | synonymous_variant | 0.18 |
gyrA | 8762 | c.1461G>C | synonymous_variant | 0.18 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491121 | c.339A>G | synonymous_variant | 0.18 |
rpoB | 760223 | c.417T>C | synonymous_variant | 0.19 |
rpoB | 760235 | c.429T>C | synonymous_variant | 0.19 |
rpoB | 760283 | c.477G>C | synonymous_variant | 0.21 |
rpoB | 760298 | c.492G>C | synonymous_variant | 0.24 |
rpoB | 760310 | c.504G>C | synonymous_variant | 0.26 |
rpoB | 760322 | c.516G>A | synonymous_variant | 0.25 |
rpoB | 760331 | c.525G>C | synonymous_variant | 0.25 |
rpoB | 760340 | c.534G>C | synonymous_variant | 0.26 |
rpoB | 760357 | p.Thr184Ser | missense_variant | 0.25 |
rpoB | 760361 | c.555T>C | synonymous_variant | 0.23 |
rpoB | 760370 | c.564C>G | synonymous_variant | 0.23 |
rpoB | 760376 | p.Asp190Glu | missense_variant | 0.22 |
rpoB | 760380 | p.Thr192Leu | missense_variant | 0.23 |
rpoB | 760418 | c.612G>C | synonymous_variant | 0.22 |
rpoB | 760424 | c.618C>G | synonymous_variant | 0.21 |
rpoB | 760430 | c.624T>C | synonymous_variant | 0.2 |
rpoB | 761765 | c.1959T>C | synonymous_variant | 0.19 |
rpoB | 761772 | p.His656Ala | missense_variant | 0.19 |
rpoB | 761778 | p.Asn658Asp | missense_variant | 0.19 |
rpoB | 761791 | p.Arg662His | missense_variant | 0.19 |
rpoB | 761813 | c.2007T>C | synonymous_variant | 0.22 |
rpoB | 761815 | p.Ala670Glu | missense_variant | 0.21 |
rpoB | 761834 | c.2028T>C | synonymous_variant | 0.2 |
rpoB | 762140 | c.2334G>C | synonymous_variant | 0.18 |
rpoB | 762161 | c.2355C>G | synonymous_variant | 0.18 |
rpoB | 762185 | c.2379G>C | synonymous_variant | 0.19 |
rpoC | 764431 | c.1062G>C | synonymous_variant | 0.18 |
rpoC | 764575 | c.1206T>C | synonymous_variant | 0.18 |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.18 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 765734 | c.2365_2367delTTGinsCTC | synonymous_variant | 0.19 |
rpoC | 765739 | c.2370G>C | synonymous_variant | 0.2 |
rpoC | 765751 | c.2382C>G | synonymous_variant | 0.21 |
rpoC | 765753 | p.Asp795Ala | missense_variant | 0.23 |
rpoC | 765772 | c.2403C>G | synonymous_variant | 0.21 |
rpoC | 765784 | c.2415C>G | synonymous_variant | 0.2 |
rpoC | 765793 | c.2424C>G | synonymous_variant | 0.2 |
rpoC | 765796 | c.2427C>T | synonymous_variant | 0.2 |
rpoC | 765811 | c.2442T>G | synonymous_variant | 0.21 |
rpoC | 765826 | c.2457T>C | synonymous_variant | 0.22 |
rpoC | 765835 | c.2466C>T | synonymous_variant | 0.22 |
rpoC | 765850 | c.2481G>C | synonymous_variant | 0.25 |
rpoC | 765871 | c.2502T>C | synonymous_variant | 0.21 |
rpoC | 765883 | c.2514C>G | synonymous_variant | 0.19 |
rpoC | 765886 | c.2517C>G | synonymous_variant | 0.2 |
rpoC | 765892 | c.2523T>C | synonymous_variant | 0.2 |
rpoC | 766522 | c.3153C>A | synonymous_variant | 0.2 |
rpoC | 766525 | c.3156G>T | synonymous_variant | 0.2 |
rpoC | 766540 | p.Asp1057Glu | missense_variant | 0.23 |
rpoC | 766543 | c.3174C>T | synonymous_variant | 0.21 |
rpoC | 766549 | c.3180G>C | synonymous_variant | 0.22 |
rpoC | 766573 | c.3204T>C | synonymous_variant | 0.25 |
rpoC | 766582 | c.3213C>G | synonymous_variant | 0.23 |
rpoC | 766583 | p.Gly1072Ser | missense_variant | 0.23 |
rpoC | 766591 | c.3222A>G | synonymous_variant | 0.24 |
rpoC | 766594 | c.3225G>C | synonymous_variant | 0.25 |
rpoC | 766597 | c.3228C>G | synonymous_variant | 0.25 |
rpoC | 766607 | p.Ile1080Leu | missense_variant | 0.28 |
rpoC | 766645 | c.3276A>G | synonymous_variant | 0.28 |
rpoC | 766657 | c.3288A>G | synonymous_variant | 0.29 |
rpoC | 766660 | c.3291G>A | synonymous_variant | 0.29 |
rpoC | 766666 | c.3297C>T | synonymous_variant | 0.26 |
rpoC | 766672 | c.3303T>C | synonymous_variant | 0.25 |
rpoC | 766693 | c.3324C>T | synonymous_variant | 0.25 |
rpoC | 766726 | c.3357T>C | synonymous_variant | 0.25 |
rpoC | 766733 | c.3364C>T | synonymous_variant | 0.24 |
rpoC | 766738 | c.3369G>C | synonymous_variant | 0.19 |
rpoC | 766765 | c.3396A>C | synonymous_variant | 0.2 |
rpoC | 766774 | c.3405T>C | synonymous_variant | 0.22 |
rpoC | 766801 | c.3432C>T | synonymous_variant | 0.22 |
rpoC | 766804 | c.3435A>G | synonymous_variant | 0.25 |
rpoC | 766837 | c.3468G>C | synonymous_variant | 0.27 |
rpoC | 766864 | c.3495G>C | synonymous_variant | 0.25 |
rpoC | 766894 | c.3525T>C | synonymous_variant | 0.27 |
rpoC | 766895 | c.3526T>C | synonymous_variant | 0.26 |
rpoC | 766900 | c.3531T>C | synonymous_variant | 0.27 |
rpoC | 766918 | c.3549C>T | synonymous_variant | 0.26 |
rpoC | 766933 | c.3564A>G | synonymous_variant | 0.23 |
rpoC | 766934 | p.Glu1189Ser | missense_variant | 0.22 |
rpoC | 766945 | c.3576A>C | synonymous_variant | 0.24 |
rpoC | 766963 | c.3594T>C | synonymous_variant | 0.24 |
rpoC | 766972 | c.3603G>C | synonymous_variant | 0.25 |
rpoC | 766978 | c.3609C>T | synonymous_variant | 0.22 |
rpoC | 766996 | c.3627C>T | synonymous_variant | 0.23 |
rpoC | 767009 | c.3640_3642delTCGinsAGC | synonymous_variant | 0.2 |
rpoC | 767014 | c.3645G>C | synonymous_variant | 0.2 |
rpoC | 767035 | c.3666G>C | synonymous_variant | 0.21 |
rpoC | 767059 | c.3690T>G | synonymous_variant | 0.21 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.99 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781760 | c.201T>C | synonymous_variant | 0.17 |
rpsL | 781793 | c.234G>C | synonymous_variant | 0.19 |
rpsL | 781832 | c.273T>G | synonymous_variant | 0.2 |
fbiC | 1303331 | p.Arg134Gln | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472970 | n.1125C>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472978 | n.1133T>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1473105 | n.1260G>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1473840 | n.183A>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1473877 | n.220G>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.24 |
rrl | 1473917 | n.260G>A | non_coding_transcript_exon_variant | 0.22 |
rrl | 1473943 | n.286G>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1473945 | n.288T>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1473946 | n.289A>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1473986 | n.329T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1473987 | n.330G>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1473995 | n.338G>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474009 | n.352A>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474012 | n.355C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1474049 | n.392G>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474093 | n.436G>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474099 | n.442G>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474103 | n.446A>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1474181 | n.524C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474201 | n.544T>C | non_coding_transcript_exon_variant | 0.23 |
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1474291 | n.635_649delTTCCTCTCCGGAGGA | non_coding_transcript_exon_variant | 0.25 |
rrl | 1474308 | n.651G>T | non_coding_transcript_exon_variant | 0.24 |
rrl | 1474310 | n.653T>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474356 | n.699T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1474362 | n.705A>G | non_coding_transcript_exon_variant | 0.23 |
rrl | 1474376 | n.719T>C | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474956 | n.1299C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1474961 | n.1304T>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474963 | n.1306G>A | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474964 | n.1307T>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1474970 | n.1313G>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475006 | n.1349A>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475028 | n.1371G>A | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475061 | n.1404C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475088 | n.1431A>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475199 | n.1542G>A | non_coding_transcript_exon_variant | 0.28 |
rrl | 1475206 | n.1549C>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1475209 | n.1552G>C | non_coding_transcript_exon_variant | 0.3 |
rrl | 1475213 | n.1556C>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1475249 | n.1592T>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1475252 | n.1595C>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475266 | n.1609T>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475273 | n.1616T>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475275 | n.1618C>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475276 | n.1619T>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475279 | n.1622G>C | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475291 | n.1634A>C | non_coding_transcript_exon_variant | 0.28 |
rrl | 1475315 | n.1658A>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1475355 | n.1698C>T | non_coding_transcript_exon_variant | 0.28 |
rrl | 1475369 | n.1712G>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475483 | n.1826C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475608 | n.1951T>C | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475642 | n.1985T>C | non_coding_transcript_exon_variant | 0.19 |
inhA | 1674600 | c.399G>T | synonymous_variant | 0.19 |
rpsA | 1833787 | c.246C>G | synonymous_variant | 0.19 |
rpsA | 1833790 | c.249T>A | synonymous_variant | 0.19 |
rpsA | 1833811 | c.270G>C | synonymous_variant | 0.18 |
rpsA | 1834246 | c.705G>C | synonymous_variant | 0.19 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289017 | c.225T>C | synonymous_variant | 1.0 |
kasA | 2518609 | p.Met165Ile | missense_variant | 0.19 |
kasA | 2518618 | c.504G>T | synonymous_variant | 0.2 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.98 |
fbiA | 3641038 | p.Ala166Thr | missense_variant | 1.0 |
rpoA | 3878094 | c.412_414delCTCinsTTG | synonymous_variant | 0.2 |
rpoA | 3878100 | c.408C>G | synonymous_variant | 0.21 |
rpoA | 3878106 | c.402G>C | synonymous_variant | 0.2 |
rpoA | 3878118 | c.390T>C | synonymous_variant | 0.2 |
rpoA | 3878130 | c.378C>G | synonymous_variant | 0.2 |
rpoA | 3878141 | p.Met123Leu | missense_variant | 0.2 |
rpoA | 3878142 | p.Gly122Glu | missense_variant | 0.2 |
rpoA | 3878157 | c.351C>G | synonymous_variant | 0.2 |
rpoA | 3878163 | c.345C>T | synonymous_variant | 0.22 |
rpoA | 3878169 | c.339G>C | synonymous_variant | 0.22 |
rpoA | 3878172 | c.336G>C | synonymous_variant | 0.24 |
rpoA | 3878187 | c.321C>A | synonymous_variant | 0.23 |
rpoA | 3878193 | c.315T>C | synonymous_variant | 0.21 |
rpoA | 3878197 | p.Glu104Ala | missense_variant | 0.23 |
rpoA | 3878205 | c.303T>C | synonymous_variant | 0.22 |
rpoA | 3878217 | c.291A>G | synonymous_variant | 0.21 |
rpoA | 3878220 | c.288C>T | synonymous_variant | 0.2 |
rpoA | 3878247 | c.261G>C | synonymous_variant | 0.19 |
rpoA | 3878253 | c.255G>C | synonymous_variant | 0.2 |
rpoA | 3878271 | c.237T>C | synonymous_variant | 0.21 |
rpoA | 3878284 | p.Glu75Ala | missense_variant | 0.18 |
rpoA | 3878292 | c.216T>C | synonymous_variant | 0.19 |
rpoA | 3878298 | c.210A>G | synonymous_variant | 0.19 |
rpoA | 3878313 | c.195G>C | synonymous_variant | 0.18 |
rpoA | 3878337 | c.171T>C | synonymous_variant | 0.19 |
rpoA | 3878346 | c.162T>C | synonymous_variant | 0.21 |
rpoA | 3878361 | c.147G>C | synonymous_variant | 0.22 |
rpoA | 3878364 | c.144A>C | synonymous_variant | 0.22 |
rpoA | 3878367 | c.141C>G | synonymous_variant | 0.23 |
rpoA | 3878376 | c.132G>C | synonymous_variant | 0.2 |
rpoA | 3878385 | c.123C>G | synonymous_variant | 0.2 |
rpoA | 3878388 | c.120C>G | synonymous_variant | 0.2 |
rpoA | 3878391 | c.117T>C | synonymous_variant | 0.2 |
rpoA | 3878396 | c.112C>T | synonymous_variant | 0.2 |
rpoA | 3878415 | c.93C>T | synonymous_variant | 0.21 |
rpoA | 3878442 | c.66G>C | synonymous_variant | 0.17 |
rpoA | 3878454 | c.54A>C | synonymous_variant | 0.21 |
clpC1 | 4038755 | c.1950G>T | synonymous_variant | 0.19 |
clpC1 | 4038773 | c.1932T>C | synonymous_variant | 0.23 |
clpC1 | 4038782 | c.1923G>C | synonymous_variant | 0.22 |
clpC1 | 4038790 | c.1915C>T | synonymous_variant | 0.23 |
clpC1 | 4038812 | c.1893T>C | synonymous_variant | 0.23 |
clpC1 | 4038845 | c.1860G>C | synonymous_variant | 0.25 |
clpC1 | 4038848 | c.1857C>T | synonymous_variant | 0.25 |
clpC1 | 4038860 | c.1845G>C | synonymous_variant | 0.24 |
clpC1 | 4038878 | c.1827A>G | synonymous_variant | 0.21 |
clpC1 | 4039226 | c.1479T>C | synonymous_variant | 0.19 |
clpC1 | 4039268 | c.1437C>G | synonymous_variant | 0.19 |
clpC1 | 4039280 | c.1425G>C | synonymous_variant | 0.19 |
clpC1 | 4039286 | c.1419T>C | synonymous_variant | 0.18 |
clpC1 | 4039349 | c.1356C>T | synonymous_variant | 0.18 |
clpC1 | 4039364 | c.1341C>G | synonymous_variant | 0.2 |
clpC1 | 4039391 | c.1314T>G | synonymous_variant | 0.2 |
clpC1 | 4039397 | c.1308A>G | synonymous_variant | 0.2 |
clpC1 | 4039409 | c.1296T>C | synonymous_variant | 0.2 |
clpC1 | 4039439 | c.1266C>T | synonymous_variant | 0.2 |
clpC1 | 4039442 | c.1263A>G | synonymous_variant | 0.2 |
clpC1 | 4039454 | c.1251A>G | synonymous_variant | 0.23 |
clpC1 | 4039463 | c.1242C>G | synonymous_variant | 0.21 |
clpC1 | 4039466 | c.1239T>C | synonymous_variant | 0.22 |
clpC1 | 4039469 | c.1236T>C | synonymous_variant | 0.22 |
clpC1 | 4039481 | c.1224T>C | synonymous_variant | 0.26 |
clpC1 | 4039484 | c.1221T>C | synonymous_variant | 0.24 |
clpC1 | 4039517 | c.1188C>G | synonymous_variant | 0.21 |
clpC1 | 4039541 | c.1164C>T | synonymous_variant | 0.2 |
clpC1 | 4039556 | c.1149G>C | synonymous_variant | 0.21 |
clpC1 | 4039559 | c.1146C>G | synonymous_variant | 0.21 |
clpC1 | 4039562 | c.1143C>G | synonymous_variant | 0.2 |
clpC1 | 4039565 | c.1140G>C | synonymous_variant | 0.21 |
clpC1 | 4039570 | p.Met379Leu | missense_variant | 0.21 |
clpC1 | 4039571 | c.1134G>A | synonymous_variant | 0.2 |
clpC1 | 4039576 | p.Ala377Pro | missense_variant | 0.2 |
clpC1 | 4039577 | c.1128T>C | synonymous_variant | 0.21 |
clpC1 | 4039586 | c.1119G>C | synonymous_variant | 0.2 |
clpC1 | 4039601 | c.1104G>A | synonymous_variant | 0.2 |
clpC1 | 4039610 | c.1095G>C | synonymous_variant | 0.2 |
clpC1 | 4040267 | c.438A>G | synonymous_variant | 0.2 |
clpC1 | 4040278 | p.Ser143Thr | missense_variant | 0.18 |
clpC1 | 4040279 | c.426C>G | synonymous_variant | 0.18 |
clpC1 | 4040291 | c.414G>C | synonymous_variant | 0.18 |
embC | 4240819 | c.957A>G | synonymous_variant | 0.2 |
embC | 4240828 | c.966G>C | synonymous_variant | 0.2 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.92 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.86 |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.96 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407714 | p.Lys163Asn | missense_variant | 0.98 |