TB-Profiler result

Run: SRR13861224
Summary

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

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 0.98
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
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
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
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