Run ID: SRR8651642
Sample name:
Date: 2024-10-04T18:48:06.294753
Number of reads: 1380421
Percentage reads mapped: 99.58
Median coverage: 61.0
Strain: lineage4.5
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.5 | Euro-American | RD122 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Asp435Val | Assoc w R | |
isoniazid | katG | c.2044_2045insT | Assoc w R | High-level resistance |
ahpC | c.-81C>T | Uncertain significance | Mutation from literature | |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Asp461His | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrB | p.Asp461His | Assoc w R - Interim | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.1299dupG | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6620 | p.Asp461His | missense_variant | 1.0 | levofloxacin | Assoc w R - Interim | |
moxifloxacin | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
rpoB | 761110 | p.Asp435Val | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2154067 | c.2044_2045insT | frameshift_variant | 0.98 | isoniazid | Assoc w R | High-level resistance |
ahpC | 2726112 | c.-81C>T | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
ethA | 4326174 | c.1299dupG | frameshift_variant | 1.0 | ethionamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
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 | 7774 | p.Gly158Val | missense_variant | 0.44 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7892 | c.591G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13394 | p.Trp55* | stop_gained | 1.0 | isoniazid | Uncertain significance |
mshA | 575726 | p.Thr127Pro | missense_variant | 1.0 | isoniazid | |
ethionamide | ||||||
mshA | 575729 | p.Gln128Met | missense_variant | 0.98 | isoniazid | |
ethionamide | ||||||
ccsA | 620029 | c.139C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
rpoC | 764452 | c.1083T>C | synonymous_variant | 1.0 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776157 | p.Asp775Gly | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1253846 | p.Ala230Asp | missense_variant | 0.95 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
embR | 1416613 | c.734dupC | frameshift_variant | 0.96 | ethambutol | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
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 |
tlyA | 1918226 | p.Phe96Ser | missense_variant | 1.0 | capreomycin | |
PPE35 | 2170568 | p.Ile15Met | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2221919 | p.Val416Met | missense_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
pncA | 2288925 | p.Phe106Cys | missense_variant | 1.0 | pyrazinamide | |
lpqB | 3624893 | c.18G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
fbiA | 3640255 | c.-288_-287insA | upstream_gene_variant | 0.85 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
rpoA | 3879070 | c.-563G>A | upstream_gene_variant | 1.0 | rifampicin | |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4246163 | c.-351G>A | upstream_gene_variant | 1.0 | ethambutol | |
embB | 4247723 | p.Pro404Thr | missense_variant | 1.0 | ethambutol | |
ubiA | 4269671 | p.Val55Leu | missense_variant | 1.0 | ethambutol | Uncertain significance |
whiB6 | 4338421 | c.100delT | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
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 | 4408217 | c.-15C>T | upstream_gene_variant | 1.0 | streptomycin |