Run ID: SRR25827542
Sample name:
Date: 2024-04-15T18:09:21.058305
Number of reads: 4956895
Percentage reads mapped: 99.4
Median coverage: 166.0
Strain: lineage4.4.1.2
Spoligotype:
Drug-resistance: XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.4.1.2 | Euro-American | None | 0.99 |
lineage4.4.1 | Euro-American (S-type) | None | 0.99 |
lineage4 | Euro-American | None | 1.0 |
lineage4.4 | Euro-American | None | 0.99 |
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.Gln497Arg | Assoc w R | |
pyrazinamide | pncA | c.496dupG | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Ala | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Ala | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1401A>G | Assoc w R | |
capreomycin | rrs | n.1401A>G | Assoc w R | |
kanamycin | rrs | n.1401A>G | Assoc w R | |
cycloserine | ||||
ethionamide | ethA | c.1370_1371dupTG | Assoc w R | |
clofazimine | mmpR5 | c.144dupC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | mmpR5 | c.144dupC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
linezolid | rplC | p.Cys154Arg | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
levofloxacin | Assoc w R | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
mmpR5 | 779130 | c.144dupC | frameshift_variant | 0.97 | bedaquiline | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
clofazimine | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | |||||
rplC | 801268 | p.Cys154Arg | missense_variant | 0.99 | linezolid | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin | Assoc w R | |
amikacin | Assoc w R | ||||||
capreomycin | Assoc w R | ||||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.97 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288745 | c.496dupG | frameshift_variant | 0.99 | pyrazinamide | Assoc w R | |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.99 | ethambutol | Assoc w R | |
ethA | 4326102 | c.1370_1371dupTG | frameshift_variant | 0.98 | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
rpoC | 764817 | p.Val483Gly | 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 |
Rv1258c | 1406451 | p.Thr297Ile | missense_variant | 1.0 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.99 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.99 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
bacA | 2063063 | c.1639_1666delTGGGCCAAGGTGCTCTCCCCCGGTGAGCinsA | missense_variant&conservative_inframe_deletion | 0.97 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
ndh | 2102990 | p.Val18Ala | missense_variant | 0.98 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Not assoc w R | |||||
PPE35 | 2167770 | p.Ser948Ile | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 1.0 | pyrazinamide | 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 | |||||
folC | 2747479 | p.Glu40Asp | missense_variant | 0.54 | para-aminosalicylic_acid | |
pepQ | 2860213 | p.Pro69Leu | missense_variant | 0.98 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
thyA | 3073723 | p.Asn250Ser | missense_variant | 0.24 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiB | 3642528 | p.Glu332Lys | missense_variant | 0.99 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | ||||||
clpC1 | 4039991 | c.714G>A | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
embC | 4238963 | c.-900C>T | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.21 | ethambutol | |
embB | 4249012 | c.2499G>A | synonymous_variant | 0.98 | ethambutol | Not assoc w R |
aftB | 4267939 | p.Arg300Trp | missense_variant | 0.99 | ethambutol | 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 | ||||||
gid | 4408186 | p.Pro6Arg | missense_variant | 1.0 | streptomycin | Uncertain significance |