TB-Profiler result

Run: SRR13861235
Summary

Run ID: SRR13861235

Sample name:

Date: 2025-09-15T16:22:55.838019

Number of reads: 2629915

Percentage reads mapped: 43.88

Median coverage: 91.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 100.0
lineage4.9 Euro-American (H37Rv-like) None 100.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Gly234Glu Uncertain significance Mutation from literature
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
katG 2155411 p.Gly234Glu missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
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
gyrA 7760 c.459C>T synonymous_variant 0.12 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13524 p.Gly12Ala missense_variant 1.0 isoniazid Uncertain significance
mshA 576259 c.912C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ccsA 620690 p.Val267Glu missense_variant 0.89 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
Rv0565c 657622 c.-152G>A upstream_gene_variant 0.94 ethionamide Uncertain significance
mmaA3 738209 c.-60A>T upstream_gene_variant 1.0 isoniazid Uncertain significance
rpoB 759805 c.-2T>C upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoB 761961 p.Pro719Thr missense_variant 0.88 rifampicin Uncertain significance
rpoC 763528 c.159G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764895 p.Ile509Thr missense_variant 0.92 rifampicin Uncertain significance
rpoC 766672 c.3303T>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766726 c.3357T>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766738 c.3369G>T synonymous_variant 0.16 rifampicin Uncertain significance
rpoC 766765 c.3396A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoC 766801 c.3432C>A synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 766804 c.3435A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
mmpL5 777574 p.Phe303Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 777578 c.903C>G synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 778982 c.-502A>C upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 801169 p.Lys121* stop_gained 0.93 linezolid Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.13 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474052 n.395G>T non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476479 n.2822T>G non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834375 c.834G>A synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834417 c.876G>C synonymous_variant 0.15 pyrazinamide Uncertain significance
rpsA 1834423 c.882G>C synonymous_variant 0.15 pyrazinamide Uncertain significance
rpsA 1834435 c.894G>C synonymous_variant 0.15 pyrazinamide Uncertain significance
tlyA 1918432 p.Pro165Thr missense_variant 1.0 capreomycin Uncertain significance
ndh 2101769 p.Arg425His missense_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2155508 p.Ala202Ser missense_variant 1.0 isoniazid Uncertain significance
pncA 2289474 c.-233C>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
kasA 2518519 c.405G>C synonymous_variant 0.13 isoniazid Uncertain significance
kasA 2518540 c.426T>G synonymous_variant 0.14 isoniazid Uncertain significance
folC 2746862 p.Leu246Arg missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
folC 2747268 p.Asp111His missense_variant 0.96 para-aminosalicylic_acid Uncertain significance
Rv2752c 3065109 c.1083A>G synonymous_variant 0.99 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066839 c.-648A>G upstream_gene_variant 0.13 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
whiB7 3568816 c.-137C>T upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
whiB7 3569222 c.-543G>A upstream_gene_variant 0.99 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
lpqB 3624508 p.Ile135Val missense_variant 0.97 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625247 p.Arg456Pro missense_variant 0.97 bedaquiline Uncertain significance
rifampicin Uncertain significance
rpoA 3878049 c.459G>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoA 3878055 c.453A>G synonymous_variant 0.15 rifampicin Uncertain significance
rpoA 3878061 c.447G>C synonymous_variant 0.16 rifampicin Uncertain significance
rpoA 3878067 c.441C>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoA 3878070 c.438T>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoA 3878082 c.426T>C synonymous_variant 0.14 rifampicin Uncertain significance
clpC1 4038468 p.Asp746Gly missense_variant 0.89 pyrazinamide Uncertain significance
clpC1 4038536 c.2169C>T synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4039085 c.1620A>G synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039090 c.1615C>T synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039097 c.1608G>C synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039103 c.1602T>C synonymous_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039106 c.1599G>C synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039112 c.1593C>G synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039142 c.1563A>G synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039145 c.1560G>C synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039169 p.Glu512Asp missense_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039172 c.1533A>G synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4039178 c.1527G>C synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039183 c.1522T>C synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4040148 p.Lys186Ile missense_variant 0.96 pyrazinamide Uncertain significance
embC 4240125 p.Cys88Tyr missense_variant 0.95 ethambutol Uncertain significance
embC 4240726 c.864G>C synonymous_variant 0.13 ethambutol Not assoc w R - Interim
embC 4240780 c.918T>C synonymous_variant 0.15 ethambutol Uncertain significance
embC 4240783 c.921G>C synonymous_variant 0.16 ethambutol Uncertain significance
embC 4240789 c.927T>C synonymous_variant 0.16 ethambutol Uncertain significance
embB 4248085 c.1572T>C synonymous_variant 0.15 ethambutol Uncertain significance
embB 4248097 c.1584C>G synonymous_variant 0.16 ethambutol Uncertain significance
embB 4248118 c.1605T>C synonymous_variant 0.13 ethambutol Uncertain significance
embB 4248157 c.1644A>G synonymous_variant 0.14 ethambutol Not assoc w R - Interim
embB 4248208 p.Ser565Arg missense_variant 0.15 ethambutol Uncertain significance
embB 4248220 c.1707A>G synonymous_variant 0.17 ethambutol Not assoc w R - Interim
embB 4248241 c.1728C>T synonymous_variant 0.19 ethambutol Uncertain significance
embB 4248265 c.1752C>T synonymous_variant 0.16 ethambutol Uncertain significance
embB 4248266 c.1753C>T synonymous_variant 0.17 ethambutol Uncertain significance
embB 4248277 c.1764G>C synonymous_variant 0.15 ethambutol Uncertain significance
ethR 4327643 p.Thr32Ile missense_variant 0.99 ethionamide Uncertain significance