TB-Profiler result

Run: SRR13861168
Summary

Run ID: SRR13861168

Sample name:

Date: 2024-10-05T11:41:47.916105

Number of reads: 1215768

Percentage reads mapped: 40.56

Median coverage: 42.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: RR-TB

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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 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu443Phe Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
rpoB 761135 p.Leu443Phe missense_variant 0.17 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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 715 p.Thr239Pro missense_variant 0.95 isoniazid
gyrA 8225 c.924T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8234 c.933T>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8235 c.934_936delTTAinsCTG synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8253 p.Ile318Leu missense_variant 0.15 levofloxacin
moxifloxacin
gyrA 8264 c.963T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
fgd1 490955 p.Met58Arg missense_variant 0.98 pretomanid
delamanid
clofazimine
mshA 574818 c.-530G>C upstream_gene_variant 0.98 isoniazid
ethionamide
hadA 731861 c.-69G>C upstream_gene_variant 1.0 isoniazid
rpoB 760925 c.1119T>C synonymous_variant 0.14 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.14 rifampicin
rpoB 761150 c.1344A>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761168 c.1362C>G synonymous_variant 0.16 rifampicin
rpoB 761180 c.1374A>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761222 c.1416G>C synonymous_variant 0.2 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.16 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.2 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.18 rifampicin
rpoC 764923 c.1554A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764932 c.1563C>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766657 c.3288A>G synonymous_variant 0.16 rifampicin
rpoC 766843 c.3474T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpsL 781155 c.-405G>A upstream_gene_variant 1.0 streptomycin
fbiC 1304529 c.1599T>C synonymous_variant 0.95 pretomanid
delamanid
clofazimine
Rv1258c 1406845 p.Ala166Pro missense_variant 1.0 streptomycin
pyrazinamide
isoniazid
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473945 n.288T>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.54 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 0.51 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.43 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674607 p.Pro136Ser missense_variant 0.94 isoniazid
ethionamide
inhA 1674778 p.Pro193Ala missense_variant 0.97 isoniazid
ethionamide
rpsA 1833269 c.-273G>T upstream_gene_variant 1.0 pyrazinamide
rpsA 1833619 c.78A>C synonymous_variant 0.19 pyrazinamide
rpsA 1833661 c.120A>G synonymous_variant 0.17 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.13 pyrazinamide
rpsA 1834669 c.1128G>C synonymous_variant 0.13 pyrazinamide
bacA 2064115 p.Ala205Asp missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2169081 p.Leu511Ser missense_variant 1.0 pyrazinamide
PPE35 2169202 p.Ser471Pro missense_variant 1.0 pyrazinamide
Rv1979c 2222091 c.1074G>T synonymous_variant 1.0 bedaquiline
clofazimine
Rv1979c 2223306 c.-142T>A upstream_gene_variant 1.0 bedaquiline
clofazimine
pncA 2289228 p.Ile5Asn missense_variant 1.0 pyrazinamide
kasA 2518176 p.Ala21Gly missense_variant 1.0 isoniazid
kasA 2518642 c.528A>G synonymous_variant 0.14 isoniazid
kasA 2518663 c.549T>C synonymous_variant 0.13 isoniazid
kasA 2518747 c.633C>G synonymous_variant 0.18 isoniazid
eis 2714755 p.Pro193Gln missense_variant 1.0 kanamycin
amikacin
ahpC 2726324 c.132A>G synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ahpC 2726362 p.Phe57Ser missense_variant 0.97 isoniazid
Rv2477c 2783833 c.210G>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783843 p.Gly67Asp missense_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783860 p.Asp61Glu missense_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783863 c.180C>T synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783884 c.159T>C synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783920 c.123G>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
pepQ 2859580 p.Leu280Arg missense_variant 1.0 bedaquiline
clofazimine
pepQ 2859999 c.420G>T synonymous_variant 1.0 bedaquiline
clofazimine
Rv2681 2997338 c.600G>C synonymous_variant 1.0 capreomycin
thyX 3067940 c.6C>G synonymous_variant 1.0 para-aminosalicylic_acid
thyA 3074620 c.-149C>A upstream_gene_variant 1.0 para-aminosalicylic_acid
mtrB 3626051 p.Ser188Trp missense_variant 1.0 rifampicin
bedaquiline
mtrB 3627167 c.-554T>C upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3627170 c.-557C>G upstream_gene_variant 0.15 rifampicin
bedaquiline
rpoA 3878001 c.507A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
ddn 3986889 p.Phe16Val missense_variant 1.0 pretomanid
delamanid
clpC1 4039724 c.981A>G synonymous_variant 0.18 pyrazinamide
glpK 4138606 c.1150T>C synonymous_variant 0.13 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4242041 p.Met727Leu missense_variant 1.0 ethambutol
embA 4244723 p.Gln497His missense_variant 1.0 ethambutol Uncertain significance
aftB 4267979 c.858G>C synonymous_variant 1.0 ethambutol