Run ID: SRR25827452
Sample name:
Date: 2024-10-04T06:25:41.685552
Number of reads: 6755812
Percentage reads mapped: 93.95
Median coverage: 228.0
Strain: lineage1.1.2;lineage2.2.1;lineage4.2.2.2
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.2.2 | Euro-American (Ural) | None | 0.37 |
lineage1.1.2 | Indo-Oceanic | RD239 | 0.16 |
lineage2 | East-Asian | RD105 | 0.46 |
lineage4.2 | Euro-American | None | 0.39 |
lineage1.1 | Indo-Oceanic | RD239 | 0.15 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.45 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.46 |
lineage4 | Euro-American | None | 0.36 |
lineage1 | Indo-Oceanic | RD239 | 0.16 |
lineage4.2.2.2 | Euro-American (Ural) | None | 0.36 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embA | c.-12C>T | Uncertain significance | Mutation from literature |
embB | p.Met306Val | Assoc w R | ||
p.Gln853Pro | Uncertain significance | Mutation from literature | ||
pyrazinamide | pncA | p.Leu159Arg | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | thyX | c.-16C>T | Mutation from literature | |
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.51 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.38 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.52 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288766 | p.Leu159Arg | missense_variant | 0.31 | pyrazinamide | Assoc w R | |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 0.28 | para-aminosalicylic_acid | Mutation from literature | |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 0.22 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4247429 | p.Met306Val | missense_variant | 0.23 | ethambutol | Assoc w R | |
embB | 4249071 | p.Gln853Pro | missense_variant | 0.23 | ethambutol | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.2 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrB | 6124 | c.885C>T | synonymous_variant | 0.21 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7283 | c.-19G>T | upstream_gene_variant | 0.26 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8688 | p.Ala463Ser | missense_variant | 0.38 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.2 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13298 | p.Ile87Met | missense_variant | 0.15 | isoniazid | Not assoc w R |
fgd1 | 491290 | p.Val170Met | missense_variant | 0.24 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.67 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
mshA | 574539 | c.-809C>G | upstream_gene_variant | 0.38 | isoniazid | |
ethionamide | ||||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.5 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
mshA | 576077 | c.730C>T | synonymous_variant | 0.25 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R - Interim | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.43 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.45 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.42 | ethionamide | Uncertain significance |
Rv0565c | 657425 | p.Gly16Ser | missense_variant | 0.41 | ethionamide | Uncertain significance |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.22 | ethionamide | |
rpoB | 759546 | c.-261A>G | upstream_gene_variant | 0.23 | rifampicin | Not assoc w R |
rpoB | 761006 | c.1200C>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoB | 761015 | c.1209G>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 761057 | c.1251G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 761213 | c.1407G>C | synonymous_variant | 0.15 | rifampicin | |
rpoB | 761219 | c.1413G>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoB | 761249 | c.1443A>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 763013 | c.-357C>G | upstream_gene_variant | 0.15 | rifampicin | |
rpoB | 763028 | c.3222T>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.61 | rifampicin | Not assoc w R |
rpoB | 763034 | c.3228C>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoB | 763040 | c.3234C>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoB | 763070 | c.3264T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 763136 | c.3330C>T | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 763148 | c.-222G>C | upstream_gene_variant | 0.15 | rifampicin | |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.16 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.16 | rifampicin | Not assoc w R |
rpoC | 764461 | c.1092A>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 764497 | c.1128A>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 764510 | c.1141C>T | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 764521 | c.1152T>C | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoC | 764527 | c.1158C>T | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoC | 764536 | c.1167G>C | synonymous_variant | 0.19 | rifampicin | |
rpoC | 764539 | c.1170C>G | synonymous_variant | 0.22 | rifampicin | Not assoc w R - Interim |
rpoC | 764554 | c.1185C>T | synonymous_variant | 0.17 | rifampicin | |
rpoC | 764560 | c.1191T>C | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoC | 764566 | c.1197C>G | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoC | 764575 | c.1206T>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 764581 | c.1212T>C | synonymous_variant | 0.18 | rifampicin | |
rpoC | 764593 | c.1224C>T | synonymous_variant | 0.17 | rifampicin | |
rpoC | 764611 | c.1242G>T | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoC | 764652 | p.Ser428Trp | missense_variant | 0.15 | rifampicin | |
rpoC | 764858 | c.1489T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 764888 | c.1519T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.16 | rifampicin | Not assoc w R |
rpoC | 765700 | c.2331T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 765734 | c.2365T>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 766630 | c.3261G>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 766657 | c.3288A>G | synonymous_variant | 0.15 | rifampicin | |
rpoC | 766672 | c.3303T>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 766726 | c.3357T>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 766738 | c.3369G>C | synonymous_variant | 0.14 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.65 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.5 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpL5 | 776395 | p.Phe696Leu | missense_variant | 0.15 | bedaquiline | Uncertain significance |
clofazimine | Not assoc w R | |||||
mmpS5 | 778883 | p.Ala8Val | missense_variant | 0.16 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.44 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800204 | c.-605T>C | upstream_gene_variant | 0.31 | linezolid | |
Rv1129c | 1253930 | p.Phe202Tyr | missense_variant | 0.37 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.66 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
Rv1129c | 1254583 | c.-49A>G | upstream_gene_variant | 0.36 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.4 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
Rv1258c | 1406878 | p.Ile155Val | missense_variant | 0.18 | streptomycin | |
pyrazinamide | ||||||
isoniazid | ||||||
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.15 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.2 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472977 | n.1132G>C | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473105 | n.1260G>A | non_coding_transcript_exon_variant | 0.18 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.17 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1475765 | n.2111delG | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
linezolid | ||||||
rrl | 1476603 | n.2946G>A | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476608 | n.2951C>G | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476628 | n.2971T>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.5 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.2 | linezolid | Not assoc w R |
tsnR | 1854045 | p.Tyr147Cys | missense_variant | 0.17 | linezolid | Not assoc w R |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
bacA | 2063685 | c.1044G>A | synonymous_variant | 0.37 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R | |||||
bacA | 2063911 | p.Ile273Thr | missense_variant | 0.35 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.61 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.69 | pyrazinamide | Not assoc w R |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.19 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.19 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.15 | isoniazid | |
pepQ | 2859659 | p.Ala254Thr | missense_variant | 0.47 | bedaquiline | |
clofazimine | Uncertain significance | |||||
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.16 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 0.44 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.35 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.17 | ethionamide | Uncertain significance |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.46 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626467 | c.147G>A | synonymous_variant | 0.2 | rifampicin | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.41 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
rpoA | 3878416 | p.Gly31Ala | missense_variant | 0.22 | rifampicin | Uncertain significance |
glpK | 4138377 | p.Val460Ala | missense_variant | 0.15 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
embC | 4239593 | c.-270G>A | upstream_gene_variant | 0.2 | ethambutol | Not assoc w R |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.19 | ethambutol | Not assoc w R |
embC | 4241022 | p.Ala387Val | missense_variant | 0.26 | ethambutol | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.47 | ethambutol | Not assoc w R |
embA | 4243848 | p.Val206Met | missense_variant | 0.18 | ethambutol | Not assoc w R |
embA | 4245835 | p.Leu868Arg | missense_variant | 0.17 | ethambutol | |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.2 | ethambutol | Not assoc w R |
embB | 4249757 | p.Thr1082Ala | missense_variant | 0.22 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.29 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.18 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.15 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.6 | streptomycin | Not assoc w R |
gid | 4407620 | p.Tyr195His | missense_variant | 0.31 | streptomycin | Not assoc w R |
gid | 4407873 | c.330G>T | synonymous_variant | 0.2 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.39 | streptomycin | Not assoc w R |