Run ID: SRR13861326
Sample name:
Date: 2024-10-04T22:11:26.067138
Number of reads: 2297538
Percentage reads mapped: 57.49
Median coverage: 77.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
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 | ||||
ethambutol | embB | p.Arg460Cys | Mutation from literature | |
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 |
---|---|---|---|---|---|---|---|
embB | 4247891 | p.Arg460Cys | missense_variant | 0.93 | ethambutol | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6088 | c.849C>A | synonymous_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
hadA | 731690 | c.-240A>G | upstream_gene_variant | 1.0 | isoniazid | |
hadA | 732094 | c.165T>C | synonymous_variant | 1.0 | isoniazid | |
nusG | 734764 | p.Ala171Ser | missense_variant | 0.97 | rifampicin | |
rpoB | 760181 | c.375T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 760184 | c.378A>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 760328 | c.522G>C | synonymous_variant | 0.13 | rifampicin | |
rpoB | 760730 | c.924T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 761786 | c.1980C>T | synonymous_variant | 0.92 | rifampicin | Not assoc w R - Interim |
rpoC | 763945 | c.576T>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 763960 | c.591T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 763967 | p.Gly200Ser | missense_variant | 0.13 | rifampicin | |
rpoC | 764040 | p.Ser224Asn | missense_variant | 0.13 | rifampicin | |
rpoC | 764626 | c.1257C>T | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 764973 | p.Asp535Ala | missense_variant | 0.93 | rifampicin | |
rpoC | 766390 | c.3021C>T | synonymous_variant | 0.13 | rifampicin | |
rpoC | 766408 | c.3039C>T | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 766426 | c.3057C>T | synonymous_variant | 0.15 | rifampicin | |
rpoC | 766447 | c.3078T>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 766483 | c.3114G>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 766484 | p.Val1039Ile | missense_variant | 0.14 | rifampicin | Uncertain significance |
rpoC | 766492 | c.3123T>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 766495 | c.3126C>T | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 766522 | c.3153C>G | synonymous_variant | 0.16 | rifampicin | |
rpoC | 766528 | c.3159T>C | synonymous_variant | 0.17 | rifampicin | |
rpoC | 766531 | c.3162G>T | synonymous_variant | 0.17 | rifampicin | |
rpoC | 766543 | c.3174C>T | synonymous_variant | 0.17 | rifampicin | |
rpoC | 766549 | c.3180G>C | synonymous_variant | 0.18 | rifampicin | |
rpoC | 766573 | c.3204T>C | synonymous_variant | 0.17 | rifampicin | |
rpoC | 766583 | p.Gly1072Ser | missense_variant | 0.19 | rifampicin | |
rpoC | 766588 | c.3219G>A | synonymous_variant | 0.18 | rifampicin | |
rpoC | 766591 | c.3222A>G | synonymous_variant | 0.19 | rifampicin | |
rpoC | 766594 | c.3225G>C | synonymous_variant | 0.2 | rifampicin | |
rpoC | 766607 | p.Ile1080Leu | missense_variant | 0.17 | rifampicin | |
rpoC | 766630 | c.3261G>C | synonymous_variant | 0.17 | rifampicin | |
rpoC | 766645 | c.3276A>G | synonymous_variant | 0.16 | rifampicin | |
rpoC | 766651 | c.3282T>C | synonymous_variant | 0.18 | rifampicin | |
rpoC | 766657 | c.3288A>G | synonymous_variant | 0.16 | rifampicin | |
rpoC | 766672 | c.3303T>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 766738 | c.3369G>T | synonymous_variant | 0.12 | rifampicin | |
rpoC | 766750 | c.3381C>G | synonymous_variant | 0.14 | rifampicin | |
rpoC | 766933 | c.3564A>G | synonymous_variant | 0.14 | rifampicin | |
rpoC | 766945 | c.3576A>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 766963 | c.3594T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 766996 | c.3627C>T | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 767009 | p.Ser1214Thr | missense_variant | 0.14 | rifampicin | |
rpoC | 767014 | c.3645G>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 767033 | c.3664_3666delTCGinsAGT | synonymous_variant | 0.14 | rifampicin | |
rpoC | 767059 | c.3690T>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 767062 | c.3693C>A | synonymous_variant | 0.16 | rifampicin | |
rpoC | 767074 | c.3705T>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 767098 | c.3729T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 767119 | c.3750A>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 767134 | c.3765C>G | synonymous_variant | 0.14 | rifampicin | |
rpoC | 767158 | c.3789T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 767167 | c.3798C>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 767180 | p.Ala1271Gln | missense_variant | 0.15 | rifampicin | |
rpoC | 767191 | c.3822C>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpsL | 781532 | c.-28G>T | upstream_gene_variant | 1.0 | streptomycin | |
rplC | 800224 | c.-585G>C | upstream_gene_variant | 1.0 | linezolid | |
fbiC | 1302843 | c.-88A>C | upstream_gene_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fbiC | 1302887 | c.-43delG | upstream_gene_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
rrl | 1473434 | n.-224T>C | upstream_gene_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1473813 | n.156C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1476368 | n.2711T>A | non_coding_transcript_exon_variant | 0.91 | capreomycin | |
linezolid | ||||||
rpsA | 1833260 | c.-282G>C | upstream_gene_variant | 1.0 | pyrazinamide | |
rpsA | 1833724 | c.183C>G | synonymous_variant | 0.16 | pyrazinamide | |
rpsA | 1833727 | c.186G>C | synonymous_variant | 0.16 | pyrazinamide | |
rpsA | 1833742 | c.201A>G | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1833787 | c.246C>G | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1833790 | c.249T>A | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1833799 | c.258C>G | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1833856 | c.315A>G | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1834348 | c.807T>C | synonymous_variant | 0.14 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834366 | c.825A>G | synonymous_variant | 0.14 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834375 | c.834G>A | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834396 | c.855G>C | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834411 | c.870T>C | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1834435 | c.894G>C | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834498 | c.957C>T | synonymous_variant | 0.13 | pyrazinamide | |
katG | 2156364 | c.-253T>G | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
Rv1979c | 2221814 | p.Leu451Val | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2222030 | p.Val379Met | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
kasA | 2518687 | c.573C>T | synonymous_variant | 0.13 | isoniazid | |
kasA | 2518696 | c.582C>G | synonymous_variant | 0.13 | isoniazid | |
kasA | 2518717 | c.603C>T | synonymous_variant | 0.15 | isoniazid | |
kasA | 2518723 | p.Glu203Asp | missense_variant | 0.14 | isoniazid | |
kasA | 2518732 | c.618C>G | synonymous_variant | 0.15 | isoniazid | |
kasA | 2519238 | p.Thr375Lys | missense_variant | 1.0 | isoniazid | |
folC | 2747285 | p.Val105Ala | missense_variant | 0.97 | para-aminosalicylic_acid | |
Rv2477c | 2783110 | c.933C>A | synonymous_variant | 0.13 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783116 | c.927T>C | synonymous_variant | 0.14 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783203 | c.840C>T | synonymous_variant | 0.14 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783221 | c.822G>T | synonymous_variant | 0.14 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783243 | p.Thr267Ser | missense_variant | 0.14 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783247 | c.796T>C | synonymous_variant | 0.14 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783254 | c.789A>G | synonymous_variant | 0.15 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783263 | c.780G>C | synonymous_variant | 0.16 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783278 | c.765A>G | synonymous_variant | 0.14 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783287 | c.756C>G | synonymous_variant | 0.14 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783290 | c.753G>C | synonymous_variant | 0.13 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2783578 | p.Glu155Asp | missense_variant | 0.13 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2784556 | c.-514A>C | upstream_gene_variant | 1.0 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
pepQ | 2859712 | p.Thr236Ser | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv2681 | 2996593 | c.-146T>C | upstream_gene_variant | 1.0 | capreomycin | |
Rv2681 | 2997178 | p.Val147Glu | missense_variant | 1.0 | capreomycin | |
Rv2752c | 3065064 | c.1128G>T | synonymous_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
thyX | 3068085 | c.-140T>A | upstream_gene_variant | 0.99 | para-aminosalicylic_acid | |
ald | 3087003 | p.Asp62His | missense_variant | 1.0 | cycloserine | |
Rv3083 | 3448914 | p.Ile137Met | missense_variant | 1.0 | ethionamide | |
whiB7 | 3568676 | p.Ser2Pro | missense_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
mtrB | 3625172 | p.Thr481Ser | missense_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
lpqB | 3625687 | c.-777G>C | upstream_gene_variant | 0.13 | rifampicin | |
bedaquiline | ||||||
lpqB | 3625696 | c.-786A>G | upstream_gene_variant | 0.14 | rifampicin | |
bedaquiline | ||||||
mtrB | 3625705 | c.909C>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
bedaquiline | ||||||
lpqB | 3625714 | c.-804C>T | upstream_gene_variant | 0.17 | rifampicin | |
bedaquiline | ||||||
mtrB | 3625720 | c.894G>C | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
bedaquiline | ||||||
mtrB | 3625729 | c.885A>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
bedaquiline | ||||||
mtrB | 3625735 | c.879C>A | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
bedaquiline | ||||||
mtrB | 3625750 | c.864G>A | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
bedaquiline | ||||||
mtrB | 3625755 | p.Ala287Thr | missense_variant | 0.16 | rifampicin | Uncertain significance |
bedaquiline | ||||||
mtrB | 3625797 | p.Val273Met | missense_variant | 0.13 | rifampicin | Uncertain significance |
bedaquiline | Uncertain significance | |||||
fbiA | 3641491 | p.Ala317Pro | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
alr | 3840235 | p.Gly396* | stop_gained | 0.99 | cycloserine | |
alr | 3840304 | c.1116delT | frameshift_variant | 0.94 | cycloserine | |
alr | 3841263 | p.Arg53His | missense_variant | 1.0 | cycloserine | |
rpoA | 3878082 | c.426T>C | synonymous_variant | 0.13 | rifampicin | |
glpK | 4139790 | c.-35C>T | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
embC | 4240671 | p.Thr270Ile | missense_variant | 0.12 | ethambutol | Not assoc w R |
embC | 4240706 | p.Val282Thr | missense_variant | 0.13 | ethambutol | |
embC | 4240726 | c.864G>C | synonymous_variant | 0.15 | ethambutol | Not assoc w R - Interim |
embC | 4240789 | c.927T>C | synonymous_variant | 0.14 | ethambutol | |
embC | 4241029 | p.Trp389* | stop_gained | 0.95 | ethambutol | |
embB | 4249631 | p.Thr1040Pro | missense_variant | 0.98 | ethambutol | |
ethA | 4327197 | p.Gly93Arg | missense_variant | 1.0 | ethionamide | Uncertain significance |