Run ID: SRR13861224
Sample name:
Date: 2024-10-05T13:01:48.755144
Number of reads: 1633948
Percentage reads mapped: 27.26
Median coverage: 55.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.98 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
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 |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1242 | c.1242G>C | synonymous_variant | 0.15 | isoniazid | |
gyrB | 6624 | p.Ser462* | stop_gained | 0.97 | levofloxacin | Uncertain significance |
moxifloxacin | ||||||
gyrA | 7285 | c.-17T>C | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7637 | c.336C>G | synonymous_variant | 0.16 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7649 | c.348C>T | synonymous_variant | 0.14 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7697 | c.396C>G | synonymous_variant | 0.15 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7715 | c.414G>C | synonymous_variant | 0.14 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7728 | c.427_429delAGGinsCGC | synonymous_variant | 0.16 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7760 | c.459C>T | synonymous_variant | 0.17 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7763 | c.462T>C | synonymous_variant | 0.16 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7835 | c.534A>G | synonymous_variant | 0.21 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7838 | c.537C>G | synonymous_variant | 0.21 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7859 | c.558A>C | synonymous_variant | 0.19 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7862 | c.561C>G | synonymous_variant | 0.19 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7865 | c.564T>C | synonymous_variant | 0.19 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 8798 | c.1497C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
mmaA3 | 737872 | p.Asp93Ala | missense_variant | 1.0 | isoniazid | |
mmaA3 | 738202 | c.-53A>C | upstream_gene_variant | 1.0 | isoniazid | |
rpoB | 761222 | c.1416G>C | synonymous_variant | 0.15 | rifampicin | |
rpoB | 762218 | c.2412T>G | synonymous_variant | 0.16 | rifampicin | |
rpoB | 762254 | c.2448T>C | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
rpoB | 762266 | c.2460T>C | synonymous_variant | 0.17 | rifampicin | |
rpoB | 762284 | c.2478G>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoB | 762293 | c.2487T>C | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoB | 762317 | c.2511A>G | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoB | 762362 | p.Glu852Asp | missense_variant | 0.18 | rifampicin | |
rpoB | 762369 | c.2563T>C | synonymous_variant | 0.18 | rifampicin | |
rpoC | 762374 | c.-996G>C | upstream_gene_variant | 0.16 | rifampicin | |
rpoC | 762380 | c.-990T>G | upstream_gene_variant | 0.17 | rifampicin | |
rpoC | 762395 | c.-975G>C | upstream_gene_variant | 0.16 | rifampicin | |
rpoC | 762398 | c.-972T>C | upstream_gene_variant | 0.15 | rifampicin | |
rpoB | 762404 | c.2598T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 762410 | c.-960T>C | upstream_gene_variant | 0.17 | rifampicin | |
rpoB | 762416 | c.2610A>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 762443 | c.-927G>C | upstream_gene_variant | 0.15 | rifampicin | |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.2 | rifampicin | |
rpoB | 762995 | c.3189G>T | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoC | 763444 | c.75T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 763456 | c.87A>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 763468 | c.99G>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 763486 | c.117T>C | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
rpoC | 763528 | c.159G>A | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
rpoC | 763546 | c.177A>G | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
rpoC | 763570 | c.201G>C | synonymous_variant | 0.22 | rifampicin | Not assoc w R - Interim |
rpoC | 763594 | c.225C>T | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 763642 | c.273G>C | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
rpoC | 763658 | c.289_291delCTTinsTTG | synonymous_variant | 0.19 | rifampicin | |
rpoC | 763675 | c.306C>G | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
rpoC | 763696 | c.327T>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 763702 | c.333C>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 763708 | c.339G>A | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 763714 | c.345G>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 763717 | c.348T>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 763723 | c.354G>C | synonymous_variant | 0.17 | rifampicin | |
rpoC | 763732 | c.363C>G | synonymous_variant | 0.18 | rifampicin | |
rpoC | 763735 | c.366G>C | synonymous_variant | 0.19 | rifampicin | |
rpoC | 763744 | c.375G>C | synonymous_variant | 0.19 | rifampicin | |
rpoC | 763780 | c.411C>G | synonymous_variant | 0.15 | rifampicin | |
rpoC | 763783 | c.414G>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 764438 | c.1069_1070insA | frameshift_variant | 0.89 | rifampicin | |
rpoC | 765478 | c.2109T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 765499 | c.2130C>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 765508 | c.2139C>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 765553 | c.2184C>T | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 765556 | c.2187G>C | synonymous_variant | 0.16 | rifampicin | |
rpoC | 765559 | c.2190G>C | synonymous_variant | 0.16 | rifampicin | |
rpoC | 765578 | c.2209C>T | synonymous_variant | 0.14 | rifampicin | |
rpoC | 765583 | c.2214G>T | synonymous_variant | 0.14 | rifampicin | |
rpoC | 766384 | c.3015A>G | synonymous_variant | 0.18 | rifampicin | |
rpoC | 766390 | c.3021C>T | synonymous_variant | 0.18 | rifampicin | |
rpoC | 766408 | c.3039C>T | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 766426 | c.3057C>T | synonymous_variant | 0.17 | rifampicin | |
rpoC | 766447 | c.3078T>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 766522 | c.3153C>G | synonymous_variant | 0.18 | rifampicin | |
rpoC | 766528 | c.3159T>C | synonymous_variant | 0.13 | rifampicin | |
rpoC | 766531 | c.3162G>T | synonymous_variant | 0.13 | rifampicin | |
rpoC | 766861 | c.3492G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775795 | p.Ala896Ser | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
rpsL | 781728 | c.169T>C | synonymous_variant | 0.15 | streptomycin | |
rpsL | 781736 | c.177T>C | synonymous_variant | 0.14 | streptomycin | |
rpsL | 781754 | c.195G>C | synonymous_variant | 0.15 | streptomycin | |
rpsL | 781760 | c.201T>C | synonymous_variant | 0.18 | streptomycin | |
rpsL | 781793 | c.234G>C | synonymous_variant | 0.18 | streptomycin | |
rpsL | 781832 | c.273T>C | synonymous_variant | 0.17 | streptomycin | |
rpsL | 781841 | c.282C>G | synonymous_variant | 0.18 | streptomycin | |
rpsL | 781859 | c.300T>C | synonymous_variant | 0.16 | streptomycin | Not assoc w R - Interim |
rpsL | 781892 | c.333A>G | synonymous_variant | 0.16 | streptomycin | |
rpsL | 781898 | c.339A>T | synonymous_variant | 0.17 | streptomycin | |
rpsL | 781916 | c.357T>C | synonymous_variant | 0.13 | streptomycin | |
rplC | 800889 | c.81C>G | synonymous_variant | 0.15 | linezolid | |
fbiC | 1303593 | c.663G>A | synonymous_variant | 0.93 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
embR | 1416428 | c.919_920insT | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
rrs | 1471798 | n.-48G>A | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472913 | n.1068G>C | non_coding_transcript_exon_variant | 0.81 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.16 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473105 | n.1260G>A | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474904 | n.1247G>A | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1475006 | n.1349A>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
linezolid | ||||||
rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476167 | n.2510T>A | non_coding_transcript_exon_variant | 0.91 | capreomycin | |
linezolid | ||||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.57 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.56 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.56 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.56 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.6 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.61 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.61 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.61 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.57 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.57 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.53 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.53 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.22 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | ||||||
inhA | 1674226 | p.Arg9Trp | missense_variant | 1.0 | isoniazid | |
ethionamide | ||||||
rpsA | 1833352 | c.-190C>A | upstream_gene_variant | 1.0 | pyrazinamide | |
rpsA | 1833710 | p.Tyr57Asp | missense_variant | 0.91 | pyrazinamide | |
rpsA | 1834711 | c.1170C>T | synonymous_variant | 0.88 | pyrazinamide | |
ndh | 2102326 | c.717G>T | synonymous_variant | 1.0 | isoniazid | |
delamanid | ||||||
ethionamide | ||||||
Rv1979c | 2222739 | c.426C>A | synonymous_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2222936 | p.Ala77Thr | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
kasA | 2518687 | c.573C>T | synonymous_variant | 0.14 | isoniazid | |
kasA | 2518702 | c.588C>T | synonymous_variant | 0.13 | isoniazid | |
kasA | 2518732 | c.618C>G | synonymous_variant | 0.15 | isoniazid | |
kasA | 2518741 | c.627G>C | synonymous_variant | 0.16 | isoniazid | |
kasA | 2518747 | c.633C>G | synonymous_variant | 0.16 | isoniazid | |
eis | 2714217 | c.1115dupC | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
eis | 2714361 | c.972C>A | synonymous_variant | 1.0 | kanamycin | |
amikacin | ||||||
ahpC | 2725906 | c.-287C>G | upstream_gene_variant | 1.0 | isoniazid | |
Rv2477c | 2782975 | c.1068C>T | synonymous_variant | 0.9 | kanamycin | Not assoc w R - Interim |
levofloxacin | Not assoc w R - Interim | |||||
moxifloxacin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
ethambutol | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
pepQ | 2859813 | p.Ile202Met | missense_variant | 0.98 | bedaquiline | |
clofazimine | ||||||
pepQ | 2860286 | p.Val45Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
ribD | 2987503 | p.Gly222Val | missense_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3087394 | p.Ala192Val | missense_variant | 1.0 | cycloserine | |
ald | 3087464 | c.645C>T | synonymous_variant | 1.0 | cycloserine | |
ald | 3087512 | c.693T>A | synonymous_variant | 1.0 | cycloserine | |
Rv3083 | 3448303 | c.-201G>C | upstream_gene_variant | 1.0 | ethionamide | |
lpqB | 3623311 | p.Pro534Ser | missense_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
lpqB | 3623400 | p.Val504Glu | missense_variant | 0.98 | rifampicin | |
bedaquiline | ||||||
lpqB | 3624438 | p.Gln158Leu | missense_variant | 0.99 | rifampicin | |
bedaquiline | ||||||
mtrB | 3627122 | c.-509T>C | upstream_gene_variant | 0.15 | rifampicin | |
bedaquiline | ||||||
rpoA | 3879111 | c.-604G>C | upstream_gene_variant | 0.94 | rifampicin | |
clpC1 | 4038271 | p.Pro812Ala | missense_variant | 0.14 | pyrazinamide | |
clpC1 | 4038274 | p.Gly811Ser | missense_variant | 0.13 | pyrazinamide | |
clpC1 | 4038278 | c.2427T>C | synonymous_variant | 0.15 | pyrazinamide | |
clpC1 | 4038293 | c.2412G>C | synonymous_variant | 0.17 | pyrazinamide | |
clpC1 | 4038302 | c.2403C>G | synonymous_variant | 0.16 | pyrazinamide | |
clpC1 | 4038308 | p.Val799Ile | missense_variant | 0.15 | pyrazinamide | |
clpC1 | 4038317 | c.2388G>C | synonymous_variant | 0.15 | pyrazinamide | |
clpC1 | 4038347 | c.2358G>C | synonymous_variant | 0.17 | pyrazinamide | |
clpC1 | 4038356 | c.2349T>C | synonymous_variant | 0.15 | pyrazinamide | |
clpC1 | 4038368 | c.2337T>C | synonymous_variant | 0.15 | pyrazinamide | |
clpC1 | 4038388 | c.2317T>C | synonymous_variant | 0.15 | pyrazinamide | |
clpC1 | 4038398 | c.2307G>T | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4038956 | c.1749T>C | synonymous_variant | 0.14 | pyrazinamide | |
embC | 4241874 | p.Leu671Arg | missense_variant | 1.0 | ethambutol | |
embC | 4242816 | p.Trp985* | stop_gained | 0.98 | ethambutol | |
embB | 4248365 | p.Val618Met | missense_variant | 0.96 | ethambutol | Uncertain significance |
aftB | 4267893 | p.Ile315Ser | missense_variant | 0.98 | ethambutol | |
aftB | 4268516 | c.321A>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
ethR | 4326691 | c.-858C>A | upstream_gene_variant | 1.0 | ethionamide |