Run ID: SRR1173343
Sample name:
Date: 03-04-2023 03:22:22
Number of reads: 908604
Percentage reads mapped: 26.43
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.99 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.99 |
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 | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
ccsA | 620855 | p.Gly322Asp | missense_variant | 0.2 |
rpoB | 760589 | c.783C>T | synonymous_variant | 0.12 |
rpoB | 761051 | c.1245G>A | synonymous_variant | 0.22 |
rpoB | 761064 | p.Ala420Thr | missense_variant | 0.2 |
rpoB | 761364 | p.Asp520Tyr | missense_variant | 0.15 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763448 | p.Glu27Lys | missense_variant | 0.14 |
rpoC | 765253 | p.Ser628Arg | missense_variant | 0.2 |
rpoC | 766577 | p.Asp1070Asn | missense_variant | 0.15 |
rpoC | 766976 | p.Gly1203Ser | missense_variant | 0.14 |
rpoC | 767259 | p.Phe1297Tyr | missense_variant | 0.17 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.96 |
mmpL5 | 777367 | p.Arg372Trp | missense_variant | 0.18 |
mmpL5 | 778923 | c.-443C>T | upstream_gene_variant | 0.12 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781552 | c.-8G>A | upstream_gene_variant | 0.12 |
rpsL | 781580 | c.21G>A | synonymous_variant | 0.14 |
Rv1258c | 1406740 | p.His201Asn | missense_variant | 0.18 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472135 | n.290C>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472153 | n.308G>A | non_coding_transcript_exon_variant | 0.47 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.57 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.59 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.58 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.55 |
rrs | 1472251 | n.406G>T | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472252 | n.407G>A | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472256 | n.411T>A | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472349 | n.504A>C | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472374 | n.529T>G | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472541 | n.696T>G | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472553 | n.708C>T | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472572 | n.727T>C | non_coding_transcript_exon_variant | 0.39 |
rrs | 1472574 | n.729T>C | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472579 | n.734G>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472582 | n.737G>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472583 | n.738T>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472584 | n.739A>G | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472594 | n.749G>C | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472598 | n.753A>T | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472697 | n.852T>G | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472707 | n.862A>G | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472714 | n.869A>C | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.81 |
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.81 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.82 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.8 |
rrs | 1472825 | n.980G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473139 | n.1294T>C | non_coding_transcript_exon_variant | 0.33 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.52 |
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.62 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.75 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.75 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.76 |
rrs | 1473191 | n.1346C>T | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473198 | n.1354delC | non_coding_transcript_exon_variant | 0.8 |
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473206 | n.1361G>A | non_coding_transcript_exon_variant | 0.78 |
rrs | 1473248 | n.1403G>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1473249 | n.1404T>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1473290 | n.1445C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475133 | n.1476C>A | non_coding_transcript_exon_variant | 0.22 |
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.49 |
rrl | 1475538 | n.1881T>C | non_coding_transcript_exon_variant | 0.48 |
rrl | 1475539 | n.1882A>T | non_coding_transcript_exon_variant | 0.48 |
rrl | 1475540 | n.1883C>T | non_coding_transcript_exon_variant | 0.48 |
rrl | 1475545 | n.1888T>G | non_coding_transcript_exon_variant | 0.48 |
rrl | 1475550 | n.1893A>C | non_coding_transcript_exon_variant | 0.48 |
rrl | 1475551 | n.1894T>G | non_coding_transcript_exon_variant | 0.48 |
rrl | 1475555 | n.1898T>G | non_coding_transcript_exon_variant | 0.48 |
rrl | 1475564 | n.1907C>A | non_coding_transcript_exon_variant | 0.5 |
rrl | 1475574 | n.1917C>G | non_coding_transcript_exon_variant | 0.52 |
rrl | 1475575 | n.1918C>T | non_coding_transcript_exon_variant | 0.52 |
rrl | 1475576 | n.1919C>G | non_coding_transcript_exon_variant | 0.52 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.58 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.73 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.73 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.74 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.77 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.77 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.78 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.76 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.76 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.81 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.81 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.83 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.83 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.79 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.8 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.8 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.8 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.79 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.79 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.65 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.49 |
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.26 |
rpsA | 1833619 | c.78A>C | synonymous_variant | 0.11 |
rpsA | 1833955 | c.414G>A | synonymous_variant | 0.13 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
rpsA | 1834788 | p.Ala416Asp | missense_variant | 0.12 |
rpsA | 1834926 | p.Gly462Val | missense_variant | 0.14 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918299 | p.Trp120* | stop_gained | 0.18 |
ndh | 2102589 | c.454T>C | synonymous_variant | 0.18 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.96 |
katG | 2155193 | p.Gly307* | stop_gained | 0.13 |
katG | 2155779 | c.333C>A | synonymous_variant | 0.4 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.95 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.2 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290170 | c.-930dupG | upstream_gene_variant | 0.13 |
pncA | 2290174 | c.-933A>G | upstream_gene_variant | 0.13 |
kasA | 2518534 | c.420G>A | synonymous_variant | 0.4 |
kasA | 2518792 | c.678C>A | synonymous_variant | 0.12 |
folC | 2746790 | p.Ile270Asn | missense_variant | 0.2 |
folC | 2747750 | c.-152G>T | upstream_gene_variant | 0.12 |
pepQ | 2859416 | p.Gly335Cys | missense_variant | 0.17 |
Rv2752c | 3064772 | p.Ala474Thr | missense_variant | 0.2 |
Rv2752c | 3065716 | c.474_475delGT | frameshift_variant | 0.14 |
thyA | 3073860 | c.612C>T | synonymous_variant | 0.17 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087898 | p.Gly360Val | missense_variant | 0.22 |
ald | 3087900 | p.Val361Leu | missense_variant | 0.22 |
fbiD | 3338959 | c.-159C>G | upstream_gene_variant | 0.12 |
fbiD | 3339592 | p.His159Tyr | missense_variant | 0.15 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474352 | p.Gly116Arg | missense_variant | 0.22 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
Rv3236c | 3613163 | c.-47G>T | upstream_gene_variant | 0.12 |
fbiA | 3640609 | p.Leu23Phe | missense_variant | 0.12 |
fbiB | 3642123 | p.Glu197* | stop_gained | 0.13 |
fbiB | 3642359 | c.825C>A | synonymous_variant | 0.15 |
alr | 3840552 | p.Gly290Val | missense_variant | 0.15 |
rpoA | 3877817 | p.Gly231Cys | missense_variant | 0.17 |
ddn | 3986738 | c.-106C>A | upstream_gene_variant | 0.14 |
clpC1 | 4038255 | p.Val817Lys | missense_variant | 0.17 |
clpC1 | 4038271 | p.Pro812Ala | missense_variant | 0.12 |
clpC1 | 4038272 | p.Gly811Ser | missense_variant | 0.12 |
clpC1 | 4038275 | c.2430A>G | synonymous_variant | 0.12 |
clpC1 | 4038278 | c.2427T>C | synonymous_variant | 0.12 |
clpC1 | 4038293 | c.2412G>C | synonymous_variant | 0.14 |
clpC1 | 4039610 | c.1095G>C | synonymous_variant | 0.12 |
clpC1 | 4039616 | c.1089G>C | synonymous_variant | 0.13 |
clpC1 | 4039622 | c.1083C>T | synonymous_variant | 0.12 |
clpC1 | 4039649 | c.1056G>C | synonymous_variant | 0.15 |
clpC1 | 4039652 | c.1053G>C | synonymous_variant | 0.15 |
clpC1 | 4039670 | c.1035G>C | synonymous_variant | 0.12 |
embC | 4240654 | c.792C>A | synonymous_variant | 0.22 |
embA | 4242352 | c.-881G>T | upstream_gene_variant | 0.17 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4243112 | p.Gly1084Arg | missense_variant | 0.12 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4245407 | c.2175G>T | synonymous_variant | 0.22 |
embA | 4245857 | c.2626delG | frameshift_variant | 0.14 |
embB | 4249757 | p.Thr1082Ala | missense_variant | 0.89 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
aftB | 4268445 | p.Ala131Asp | missense_variant | 0.13 |
aftB | 4268476 | p.Gly121Trp | missense_variant | 0.18 |
ubiA | 4269239 | p.Ala199Ser | missense_variant | 0.14 |
ubiA | 4269864 | c.-31C>A | upstream_gene_variant | 0.13 |
ethA | 4326821 | p.Arg218Leu | missense_variant | 0.22 |
whiB6 | 4338239 | p.Leu95Val | missense_variant | 0.22 |
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 |
gid | 4408465 | c.-263C>A | upstream_gene_variant | 0.15 |