Run ID: SRR14782086
Sample name:
Date: 2024-10-04T05:50:55.160088
Number of reads: 2138963
Percentage reads mapped: 99.56
Median coverage: 71.0
Strain: lineage2.2.1;lineage4.2.1;lineage4.8
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.22 |
lineage4.2 | Euro-American | None | 0.3 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.18 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.21 |
lineage4 | Euro-American | None | 0.8 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.52 |
lineage4.2.1 | Euro-American (TUR) | None | 0.3 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Ser297Ala | Uncertain significance | Mutation from literature |
pyrazinamide | ||||
streptomycin | rpsL | p.Lys88Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-12C>T | Assoc w R | |
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.41 | rifampicin | Assoc w R | |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.27 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.32 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.37 | isoniazid | Assoc w R | High-level resistance |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 0.36 | kanamycin | Assoc w R | |
embB | 4247402 | p.Ser297Ala | missense_variant | 0.22 | ethambutol | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6518 | p.Val427Met | missense_variant | 0.54 | 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 | 0.49 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.52 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491247 | c.465C>T | synonymous_variant | 0.31 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.14 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
ccsA | 619969 | p.Val27Ile | missense_variant | 0.31 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.22 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.12 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.21 | rifampicin | Not assoc w R |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.29 | rifampicin | Uncertain significance |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.14 | rifampicin | Not assoc w R |
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 | 0.17 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.16 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.33 | 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 | 0.28 | linezolid | |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.16 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
sigE | 1364706 | c.294G>A | synonymous_variant | 0.17 | pyrazinamide | Not assoc w R - Interim |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.18 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.58 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rrl | 1475013 | n.1356G>A | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
linezolid | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.21 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.48 | 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 | 0.32 | 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 | 0.36 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.23 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.2 | pyrazinamide | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.53 | pyrazinamide | Not assoc w R |
PPE35 | 2169221 | c.1392T>C | synonymous_variant | 0.18 | pyrazinamide | Not assoc w R - Interim |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 0.3 | pyrazinamide | Uncertain significance |
PPE35 | 2170623 | c.-11G>A | upstream_gene_variant | 0.24 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
eis | 2714955 | c.378C>T | synonymous_variant | 0.12 | kanamycin | Not assoc w R - Interim |
amikacin | Not assoc w R - Interim | |||||
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.56 | capreomycin | |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.29 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.49 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.19 | pyrazinamide | Not assoc w R - Interim |
lpqB | 3623222 | c.1689A>G | synonymous_variant | 0.35 | rifampicin | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.53 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.14 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.28 | ethambutol | Not assoc w R |
embB | 4249594 | c.3081G>A | synonymous_variant | 0.28 | ethambutol | Not assoc w R - Interim |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.22 | ethambutol | Not assoc w R |
ethA | 4326632 | p.His281Pro | missense_variant | 0.37 | ethionamide | Uncertain significance |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 0.24 | ethionamide | |
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 | 0.42 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.26 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.25 | streptomycin | Not assoc w R |