Run ID: SRR28044341
Sample name:
Date: 2024-05-22T17:44:11.769373
Number of reads: 8117096
Percentage reads mapped: 99.51
Median coverage: 214.0
Strain: lineage4.1.1.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 1.0 |
lineage4.1.1.1 | Euro-American (X-type) | RD183 | 0.96 |
lineage4 | Euro-American | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | None | 1.0 |
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 | embB | p.Met306Ile | Assoc w R | |
pyrazinamide | pncA | p.Thr76Pro | Assoc w R | |
streptomycin | gid | c.262delG | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | folC | p.Glu40Gly | Mutation from literature | |
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | moxifloxacin | Assoc w R | High-level resistance |
levofloxacin | Assoc w R | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289016 | p.Thr76Pro | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
folC | 2747480 | p.Glu40Gly | missense_variant | 1.0 | para-aminosalicylic_acid | Mutation from literature | |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R | |
gid | 4407940 | c.262delG | frameshift_variant | 1.0 | streptomycin | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
nusG | 734315 | p.Ala21Val | missense_variant | 1.0 | rifampicin | |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 767123 | p.Val1252Leu | missense_variant | 1.0 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800219 | c.-590T>C | upstream_gene_variant | 1.0 | linezolid | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ahpC | 2726210 | c.18T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.99 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3641447 | p.Thr302Met | missense_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
rpoA | 3877553 | p.Glu319Lys | missense_variant | 1.0 | rifampicin | Not assoc w R |
embC | 4240897 | c.1035C>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243190 | c.-43G>C | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance |
embA | 4244977 | p.Gly582Ala | missense_variant | 1.0 | ethambutol | |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.23 | ethambutol | |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
whiB6 | 4338498 | p.Glu8Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin |