Run ID: SRR1062897
Sample name:
Date: 2024-04-15T09:57:17.089292
Number of reads: 1840410
Percentage reads mapped: 69.37
Median coverage: 39.0
Strain: lineage4.4.1.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.4.1 | Euro-American (S-type) | None | 0.99 |
lineage4 | Euro-American | None | 1.0 |
lineage4.4.1.1 | Euro-American | None | 1.0 |
lineage4.4 | Euro-American | 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 | |
p.Gly406Asp | Assoc w R | |||
pyrazinamide | pncA | c.390_391dupGG | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
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 | 2288850 | c.390_391dupGG | frameshift_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247431 | p.Met306Ile | missense_variant | 0.98 | ethambutol | Assoc w R | |
embB | 4247730 | p.Gly406Asp | missense_variant | 1.0 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5195 | c.-45C>G | upstream_gene_variant | 0.94 | levofloxacin | Uncertain significance |
moxifloxacin | ||||||
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 | |||||
nusG | 734851 | p.Thr200Ala | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 764605 | c.1236G>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 764611 | c.1242G>T | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoC | 764641 | c.1272C>T | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
rpoC | 764650 | c.1281G>T | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
rpoC | 764663 | p.Val432Thr | missense_variant | 0.16 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.96 | 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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.39 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472770 | n.925C>T | non_coding_transcript_exon_variant | 0.45 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.4 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.43 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.26 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>A | non_coding_transcript_exon_variant | 0.26 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476368 | n.2711T>C | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.37 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.38 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.49 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.52 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.47 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.48 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.46 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.46 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.4 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476491 | n.2834T>C | non_coding_transcript_exon_variant | 0.35 | capreomycin | |
linezolid | ||||||
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 |
ndh | 2102990 | p.Val18Ala | missense_variant | 1.0 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | 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 | 2746923 | p.Gly226Ser | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv2681 | 2997212 | c.474A>C | synonymous_variant | 1.0 | capreomycin | Not assoc w R - Interim |
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 |
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | 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 |
embA | 4243692 | p.Gly154Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4246904 | p.Val131Met | missense_variant | 0.97 | ethambutol | Uncertain significance |
ethA | 4328252 | c.-779T>G | upstream_gene_variant | 1.0 | ethionamide | |
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 | 4407758 | p.Ser149Arg | missense_variant | 1.0 | streptomycin | Uncertain significance |