Run ID: SRR1174277
Sample name:
Date: 03-04-2023 03:33:40
Number of reads: 736342
Percentage reads mapped: 25.46
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
embB | 4247729 | p.Gly406Ser | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7443 | p.Leu48Ile | missense_variant | 0.18 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8540 | c.1239C>G | synonymous_variant | 0.12 |
gyrA | 8542 | c.1242_1243insTCC | conservative_inframe_insertion | 0.13 |
gyrA | 8591 | c.1290C>A | synonymous_variant | 0.17 |
gyrA | 9107 | c.1806C>T | synonymous_variant | 0.2 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.94 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576242 | p.Gly299Cys | missense_variant | 0.15 |
ccsA | 620261 | p.Ala124Val | missense_variant | 0.22 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 759993 | p.Arg63Cys | missense_variant | 0.17 |
rpoB | 760358 | c.552C>A | synonymous_variant | 0.12 |
rpoB | 761194 | p.Gly463Val | missense_variant | 0.17 |
rpoB | 762018 | p.Glu738* | stop_gained | 0.25 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763604 | p.Gly79Cys | missense_variant | 0.17 |
rpoC | 763615 | c.246G>T | synonymous_variant | 0.14 |
rpoC | 765119 | p.Gly584Arg | missense_variant | 0.15 |
rpoC | 765136 | c.1767C>A | synonymous_variant | 0.2 |
rpoC | 766658 | p.Arg1097Trp | missense_variant | 0.18 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.91 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpR5 | 778022 | c.-968G>A | upstream_gene_variant | 0.17 |
mmpL5 | 778063 | p.Gln140* | stop_gained | 0.15 |
mmpR5 | 778121 | c.-869G>A | upstream_gene_variant | 0.22 |
mmpS5 | 778518 | p.Gly130Ser | missense_variant | 0.29 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.94 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 801278 | p.Pro157Leu | missense_variant | 0.15 |
fbiC | 1303369 | p.Leu147Ile | missense_variant | 0.12 |
Rv1258c | 1406421 | p.Phe307Ser | missense_variant | 0.15 |
Rv1258c | 1406726 | c.615C>T | synonymous_variant | 0.15 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.8 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472135 | n.290C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.46 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472153 | n.308G>A | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.63 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.65 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.64 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.63 |
rrs | 1472251 | n.406G>T | non_coding_transcript_exon_variant | 0.58 |
rrs | 1472252 | n.407G>A | non_coding_transcript_exon_variant | 0.58 |
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472256 | n.411T>A | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472277 | n.432C>G | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472349 | n.504A>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472374 | n.529T>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472553 | n.708C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472572 | n.727T>C | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472574 | n.729T>C | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472579 | n.734G>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472582 | n.737G>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472583 | n.738T>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472584 | n.739A>G | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472594 | n.749G>C | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472598 | n.753A>T | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472697 | n.852T>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472707 | n.862A>G | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472714 | n.869A>C | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.47 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.81 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.8 |
rrs | 1472825 | n.980G>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473139 | n.1294T>C | non_coding_transcript_exon_variant | 0.37 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.47 |
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.54 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.66 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.66 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.67 |
rrs | 1473191 | n.1346C>T | non_coding_transcript_exon_variant | 0.74 |
rrs | 1473198 | n.1354delC | non_coding_transcript_exon_variant | 0.71 |
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.72 |
rrs | 1473206 | n.1361G>A | non_coding_transcript_exon_variant | 0.74 |
rrl | 1475145 | n.1488C>A | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475491 | n.1834C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.67 |
rrl | 1475538 | n.1881T>C | non_coding_transcript_exon_variant | 0.68 |
rrl | 1475539 | n.1882A>T | non_coding_transcript_exon_variant | 0.68 |
rrl | 1475540 | n.1883C>T | non_coding_transcript_exon_variant | 0.68 |
rrl | 1475545 | n.1888T>G | non_coding_transcript_exon_variant | 0.68 |
rrl | 1475550 | n.1893A>C | non_coding_transcript_exon_variant | 0.68 |
rrl | 1475551 | n.1894T>G | non_coding_transcript_exon_variant | 0.7 |
rrl | 1475555 | n.1898T>G | non_coding_transcript_exon_variant | 0.72 |
rrl | 1475564 | n.1907C>A | non_coding_transcript_exon_variant | 0.72 |
rrl | 1475574 | n.1917C>G | non_coding_transcript_exon_variant | 0.72 |
rrl | 1475575 | n.1918C>T | non_coding_transcript_exon_variant | 0.72 |
rrl | 1475576 | n.1919C>G | non_coding_transcript_exon_variant | 0.72 |
rrl | 1475760 | n.2105_2106delGC | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.79 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.79 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.78 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.78 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.78 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.82 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.81 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.82 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.83 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.83 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.87 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.86 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.85 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.85 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.84 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.84 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476545 | n.2888C>G | non_coding_transcript_exon_variant | 0.12 |
inhA | 1673574 | c.-628C>A | upstream_gene_variant | 0.12 |
inhA | 1673907 | c.-295C>T | upstream_gene_variant | 0.18 |
rpsA | 1833751 | c.210C>T | synonymous_variant | 0.14 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
rpsA | 1834348 | c.807T>C | synonymous_variant | 0.15 |
rpsA | 1834396 | c.855G>A | synonymous_variant | 0.15 |
rpsA | 1834958 | p.Leu473Met | missense_variant | 0.2 |
rpsA | 1834963 | c.1422G>A | synonymous_variant | 0.18 |
tlyA | 1917748 | c.-192G>T | upstream_gene_variant | 0.17 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918083 | p.Asp48Glu | missense_variant | 0.29 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2222862 | c.303C>A | synonymous_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290131 | c.-890G>T | upstream_gene_variant | 0.17 |
kasA | 2518442 | p.Val110Phe | missense_variant | 0.12 |
kasA | 2518670 | p.Val186Met | missense_variant | 0.17 |
eis | 2714198 | p.Asp379Tyr | missense_variant | 0.15 |
eis | 2714589 | c.744G>A | synonymous_variant | 0.2 |
ahpC | 2725916 | c.-277C>A | upstream_gene_variant | 0.25 |
folC | 2746878 | p.Val241Ile | missense_variant | 0.14 |
folC | 2747542 | c.57C>A | synonymous_variant | 0.12 |
pepQ | 2859604 | p.Gly272Val | missense_variant | 0.22 |
pepQ | 2859702 | c.717G>A | synonymous_variant | 0.15 |
ribD | 2987513 | c.675C>A | synonymous_variant | 0.18 |
Rv2752c | 3065707 | p.Ala162Glu | missense_variant | 0.15 |
thyX | 3067890 | c.55delG | frameshift_variant | 0.29 |
thyA | 3074336 | p.Thr46Ser | missense_variant | 0.13 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449207 | p.Pro235Arg | missense_variant | 0.15 |
Rv3083 | 3449712 | c.1209C>T | synonymous_variant | 0.29 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475061 | p.Pro352His | missense_variant | 0.18 |
fprA | 3475234 | c.1228C>T | synonymous_variant | 0.25 |
Rv3236c | 3612077 | p.Ser347* | stop_gained | 0.2 |
Rv3236c | 3612273 | p.Val282Ile | missense_variant | 0.17 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
fbiB | 3642178 | p.Ala215Glu | missense_variant | 0.33 |
alr | 3841131 | p.Ala97Glu | missense_variant | 0.17 |
alr | 3841254 | p.Ala56Asp | missense_variant | 0.2 |
rpoA | 3878047 | p.Ala154Asp | missense_variant | 0.17 |
rpoA | 3878496 | c.12A>G | synonymous_variant | 0.29 |
rpoA | 3878666 | c.-159C>T | upstream_gene_variant | 0.33 |
ddn | 3986648 | c.-196C>G | upstream_gene_variant | 0.18 |
ddn | 3986665 | c.-179G>C | upstream_gene_variant | 0.12 |
ddn | 3987131 | c.288C>A | synonymous_variant | 0.2 |
clpC1 | 4038892 | p.Glu605* | stop_gained | 0.33 |
clpC1 | 4039636 | p.Glu357* | stop_gained | 0.13 |
clpC1 | 4040528 | c.177G>T | synonymous_variant | 0.22 |
embC | 4241534 | p.Pro558Ser | missense_variant | 0.17 |
embC | 4242073 | c.2211C>T | synonymous_variant | 0.12 |
embC | 4242339 | p.Thr826Asn | missense_variant | 0.15 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4243547 | c.315G>A | synonymous_variant | 0.15 |
embA | 4244297 | c.1065G>A | synonymous_variant | 0.33 |
embA | 4244915 | c.1683G>T | synonymous_variant | 0.13 |
embA | 4245071 | c.1839G>T | synonymous_variant | 0.12 |
embA | 4245088 | c.1859delG | frameshift_variant | 0.17 |
embA | 4245906 | p.Leu892Met | missense_variant | 0.22 |
embB | 4247626 | c.1113C>A | synonymous_variant | 0.17 |
embB | 4247916 | p.Arg468Leu | missense_variant | 0.5 |
embB | 4249757 | p.Thr1082Ala | missense_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4268023 | p.Leu272Met | missense_variant | 0.2 |
whiB6 | 4338207 | c.315G>A | synonymous_variant | 0.29 |
whiB6 | 4338577 | c.-56G>A | upstream_gene_variant | 0.14 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |