Run ID: SRR13861528
Sample name:
Date: 2024-10-05T06:18:58.066443
Number of reads: 645150
Percentage reads mapped: 64.58
Median coverage: 22.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | c.1700delT | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | ||||
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 |
---|---|---|---|---|---|---|---|
katG | 2154411 | c.1700delT | frameshift_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7949 | c.648G>T | synonymous_variant | 0.93 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 8123 | p.Leu274Phe | missense_variant | 0.88 | levofloxacin | Uncertain significance |
moxifloxacin | ||||||
gyrA | 9768 | p.Gly823Cys | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
Rv0565c | 657349 | p.Glu41Val | missense_variant | 0.96 | ethionamide | |
mmaA3 | 738066 | c.84C>T | synonymous_variant | 1.0 | isoniazid | |
rpoC | 763441 | c.72C>G | synonymous_variant | 0.3 | rifampicin | |
rpoC | 763444 | c.75T>C | synonymous_variant | 0.3 | rifampicin | Not assoc w R - Interim |
rpoC | 763456 | c.87A>G | synonymous_variant | 0.35 | rifampicin | Not assoc w R - Interim |
rpoC | 763468 | c.99G>C | synonymous_variant | 0.32 | rifampicin | Not assoc w R - Interim |
rpoC | 763486 | c.117T>C | synonymous_variant | 0.38 | rifampicin | Not assoc w R - Interim |
rpoC | 763528 | c.159G>A | synonymous_variant | 0.39 | rifampicin | Not assoc w R - Interim |
rpoC | 763546 | c.177A>G | synonymous_variant | 0.41 | rifampicin | Not assoc w R - Interim |
rpoC | 763570 | c.201G>C | synonymous_variant | 0.35 | rifampicin | Not assoc w R - Interim |
rpoC | 763734 | p.Pro122Leu | missense_variant | 0.89 | rifampicin | |
rpoC | 764098 | c.729A>G | synonymous_variant | 0.27 | rifampicin | Not assoc w R - Interim |
rpoC | 764101 | c.732C>G | synonymous_variant | 0.27 | rifampicin | Not assoc w R - Interim |
rpoC | 764131 | c.762T>C | synonymous_variant | 0.24 | rifampicin | |
rpoC | 764161 | c.792G>C | synonymous_variant | 0.28 | rifampicin | |
rpoC | 764188 | c.819A>G | synonymous_variant | 0.3 | rifampicin | Not assoc w R - Interim |
rpoC | 764195 | p.Ser276Gln | missense_variant | 0.31 | rifampicin | |
rpoC | 764203 | c.834G>T | synonymous_variant | 0.33 | rifampicin | |
rpoC | 764206 | c.837T>C | synonymous_variant | 0.33 | rifampicin | Not assoc w R - Interim |
rpoC | 764320 | c.951C>G | synonymous_variant | 0.22 | rifampicin | |
rpoC | 764911 | c.1542A>G | synonymous_variant | 0.28 | rifampicin | |
rpoC | 764923 | c.1554A>G | synonymous_variant | 0.3 | rifampicin | Not assoc w R - Interim |
rpoC | 764932 | c.1563C>A | synonymous_variant | 0.29 | rifampicin | Not assoc w R - Interim |
rpoC | 764968 | c.1599T>C | synonymous_variant | 0.32 | rifampicin | Not assoc w R - Interim |
rpsL | 781892 | c.333A>G | synonymous_variant | 0.21 | streptomycin | |
Rv1129c | 1253309 | p.His409Pro | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
rrl | 1475355 | n.1698C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475369 | n.1712G>C | non_coding_transcript_exon_variant | 0.27 | capreomycin | |
linezolid | ||||||
rrl | 1475419 | n.1762C>T | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.19 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.19 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476640 | n.2983C>A | non_coding_transcript_exon_variant | 0.88 | capreomycin | |
linezolid | ||||||
tsnR | 1853566 | c.-40C>T | upstream_gene_variant | 1.0 | linezolid | |
tlyA | 1918034 | p.Val32Ala | missense_variant | 1.0 | capreomycin | |
bacA | 2064615 | p.Leu38Phe | missense_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
katG | 2155918 | p.Ala65Val | missense_variant | 1.0 | isoniazid | |
PPE35 | 2168767 | p.Ser616Gly | missense_variant | 1.0 | pyrazinamide | |
PPE35 | 2170815 | c.-203C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
Rv1979c | 2222377 | p.Val263Gly | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
kasA | 2518723 | p.Glu203Asp | missense_variant | 0.22 | isoniazid | |
kasA | 2518732 | c.618C>G | synonymous_variant | 0.24 | isoniazid | |
kasA | 2518768 | c.654C>G | synonymous_variant | 0.23 | isoniazid | |
Rv2477c | 2783104 | c.939C>A | synonymous_variant | 0.92 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783751 | p.Ile98Val | missense_variant | 0.29 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783758 | p.Asp95Glu | missense_variant | 0.27 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783761 | c.282G>C | synonymous_variant | 0.23 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783794 | c.249G>A | synonymous_variant | 0.26 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783797 | p.Asp82Glu | missense_variant | 0.26 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783815 | c.228A>G | synonymous_variant | 0.27 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783833 | c.210G>C | synonymous_variant | 0.28 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783843 | p.Gly67Asp | missense_variant | 0.25 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783860 | p.Asp61Glu | missense_variant | 0.22 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783863 | c.180C>T | synonymous_variant | 0.22 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783920 | c.123G>C | synonymous_variant | 0.19 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
ribD | 2986993 | p.Gly52Val | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv2752c | 3065787 | c.405G>C | synonymous_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
Rv2752c | 3066807 | c.-616T>C | upstream_gene_variant | 0.21 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
Rv2752c | 3066813 | c.-622C>T | upstream_gene_variant | 0.21 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
Rv2752c | 3066819 | c.-628T>C | upstream_gene_variant | 0.21 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
Rv2752c | 3066822 | c.-631T>C | upstream_gene_variant | 0.21 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
Rv2752c | 3066839 | c.-648A>G | upstream_gene_variant | 0.19 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
Rv3083 | 3448649 | p.Arg49Pro | missense_variant | 1.0 | ethionamide | |
Rv3236c | 3613067 | p.Val17Gly | missense_variant | 1.0 | pyrazinamide | |
Rv3236c | 3613315 | c.-199T>G | upstream_gene_variant | 1.0 | pyrazinamide | |
fbiA | 3640435 | c.-108A>C | upstream_gene_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
rpoA | 3878982 | c.-475A>T | upstream_gene_variant | 1.0 | rifampicin | |
clpC1 | 4039112 | c.1593C>G | synonymous_variant | 0.2 | pyrazinamide | |
clpC1 | 4039121 | c.1584T>C | synonymous_variant | 0.2 | pyrazinamide | |
clpC1 | 4039124 | c.1581C>G | synonymous_variant | 0.2 | pyrazinamide | |
clpC1 | 4039142 | c.1563A>G | synonymous_variant | 0.22 | pyrazinamide | |
clpC1 | 4039145 | c.1560G>C | synonymous_variant | 0.21 | pyrazinamide | |
clpC1 | 4039169 | p.Glu512Asp | missense_variant | 0.23 | pyrazinamide | |
clpC1 | 4039172 | c.1533A>G | synonymous_variant | 0.23 | pyrazinamide | |
clpC1 | 4039178 | c.1527G>C | synonymous_variant | 0.25 | pyrazinamide | |
clpC1 | 4039183 | c.1522T>C | synonymous_variant | 0.25 | pyrazinamide | |
clpC1 | 4039187 | c.1518G>C | synonymous_variant | 0.28 | pyrazinamide | |
clpC1 | 4039190 | c.1515C>G | synonymous_variant | 0.25 | pyrazinamide | |
clpC1 | 4039208 | c.1497C>G | synonymous_variant | 0.23 | pyrazinamide | |
clpC1 | 4039226 | c.1479T>C | synonymous_variant | 0.21 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4039274 | c.1431G>C | synonymous_variant | 0.23 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4039286 | c.1419T>C | synonymous_variant | 0.23 | pyrazinamide | |
clpC1 | 4039289 | c.1416T>C | synonymous_variant | 0.23 | pyrazinamide | |
clpC1 | 4039295 | c.1410A>C | synonymous_variant | 0.24 | pyrazinamide | |
clpC1 | 4039298 | c.1407T>C | synonymous_variant | 0.24 | pyrazinamide | |
clpC1 | 4039842 | c.862_863insT | frameshift_variant | 1.0 | pyrazinamide | |
panD | 4044103 | p.Ile60Ser | missense_variant | 0.91 | pyrazinamide | |
embC | 4240789 | c.927T>C | synonymous_variant | 0.2 | ethambutol | |
embA | 4245031 | p.Arg600Gln | missense_variant | 1.0 | ethambutol | |
gid | 4408218 | c.-16G>T | upstream_gene_variant | 1.0 | streptomycin |