TB-Profiler result

Run: SRR29096717
Summary

Run ID: SRR29096717

Sample name:

Date: 2025-02-11T14:58:44.148515

Number of reads: 73413

Percentage reads mapped: 66.69

Median coverage: 1.0

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 0.97
lineage4.9 Euro-American (H37Rv-like) None 0.96
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
gyrA 7442 c.141G>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7451 c.150C>G synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7457 c.156T>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7463 c.162G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7466 c.165G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7469 c.168C>G synonymous_variant 0.69 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7480 p.Phe60Tyr missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 7484 c.183T>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7487 c.186C>G synonymous_variant 0.64 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7490 c.189C>T synonymous_variant 0.64 levofloxacin
moxifloxacin
gyrA 7514 c.213C>G synonymous_variant 0.92 levofloxacin
moxifloxacin
gyrA 7520 c.219G>C synonymous_variant 0.92 levofloxacin
moxifloxacin
gyrA 7526 c.225G>C synonymous_variant 0.92 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8998 p.Leu566Trp missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9017 c.1716C>T synonymous_variant 0.9 levofloxacin
moxifloxacin
rpoB 761573 c.1767C>G synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 0.95 rifampicin
rpoB 761612 c.1806G>C synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.95 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>G synonymous_variant 1.0 rifampicin
rpoB 761651 c.1845C>T synonymous_variant 0.67 rifampicin
rpoB 761657 c.1851C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 761669 c.1863C>T synonymous_variant 1.0 rifampicin
rpoB 761675 c.1869G>C synonymous_variant 1.0 rifampicin
rpoB 761690 c.1884G>C synonymous_variant 1.0 rifampicin
rpoB 761711 c.1905C>G synonymous_variant 1.0 rifampicin
rpoB 761712 p.Val636Ile missense_variant 1.0 rifampicin
rpoC 765871 c.2502T>C synonymous_variant 0.56 rifampicin
rpoC 765875 p.Val836Ile missense_variant 1.0 rifampicin Uncertain significance
rpoC 765934 c.2565C>T synonymous_variant 1.0 rifampicin
rpoC 765967 c.2598C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765973 c.2604C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765991 c.2622C>G synonymous_variant 0.7 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpsL 781929 p.Gly124Ser missense_variant 0.62 streptomycin Uncertain significance
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674542 p.Ala114Glu missense_variant 1.0 isoniazid
ethionamide
inhA 1674546 c.345T>C synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674550 p.Ser117Ala missense_variant 1.0 isoniazid
ethionamide
inhA 1674570 c.369G>C synonymous_variant 0.89 isoniazid
ethionamide
inhA 1674573 c.372G>A synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674576 c.375T>C synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674579 c.378G>C synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674585 c.384T>C synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674589 p.Met130Leu missense_variant 1.0 isoniazid
ethionamide
inhA 1674600 c.399G>C synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674601 p.Leu134Val missense_variant 0.89 isoniazid
ethionamide
inhA 1674624 c.423A>C synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674627 c.426T>G synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674639 c.438C>T synonymous_variant 0.81 isoniazid
ethionamide
inhA 1674656 p.Ser152Thr missense_variant 0.92 isoniazid
ethionamide
inhA 1674669 c.468G>C synonymous_variant 0.67 isoniazid
ethionamide
inhA 1674690 c.489C>G synonymous_variant 0.8 isoniazid
ethionamide
rpsA 1834690 c.1149T>C synonymous_variant 1.0 pyrazinamide
rpsA 1834732 c.1191T>C synonymous_variant 1.0 pyrazinamide
rpsA 1834738 p.Glu399Asp missense_variant 1.0 pyrazinamide
rpsA 1834747 c.1206A>G synonymous_variant 1.0 pyrazinamide
rpsA 1834751 p.Leu404Ile missense_variant 1.0 pyrazinamide
rpsA 1834756 c.1215G>A synonymous_variant 1.0 pyrazinamide
rpsA 1834759 c.1218A>T synonymous_variant 0.95 pyrazinamide
rpsA 1834765 p.Glu408Asp missense_variant 0.95 pyrazinamide
rpsA 1834775 p.Ala412Thr missense_variant 0.95 pyrazinamide
rpsA 1834780 c.1239A>G synonymous_variant 1.0 pyrazinamide
rpsA 1834786 c.1245A>G synonymous_variant 0.95 pyrazinamide
rpsA 1834789 c.1248T>C synonymous_variant 0.95 pyrazinamide
rpsA 1834792 c.1251G>C synonymous_variant 0.95 pyrazinamide
tsnR 1853361 c.-245T>C upstream_gene_variant 0.88 linezolid
tsnR 1853370 c.-236_-234delGCAinsTCC upstream_gene_variant 0.88 linezolid
tsnR 1853375 c.-231G>C upstream_gene_variant 0.88 linezolid
tsnR 1853387 c.-219T>G upstream_gene_variant 0.88 linezolid
tsnR 1853390 c.-216G>C upstream_gene_variant 0.88 linezolid
tsnR 1853394 c.-212_-211delCTinsGC upstream_gene_variant 0.88 linezolid
tsnR 1853420 c.-186T>G upstream_gene_variant 0.86 linezolid
tsnR 1853429 c.-177G>C upstream_gene_variant 0.77 linezolid
tsnR 1853432 c.-174G>C upstream_gene_variant 0.77 linezolid
kasA 2517917 c.-198G>T upstream_gene_variant 1.0 isoniazid
kasA 2517926 c.-189G>A upstream_gene_variant 0.96 isoniazid
kasA 2517941 c.-174C>G upstream_gene_variant 0.95 isoniazid
kasA 2517965 c.-150C>T upstream_gene_variant 0.9 isoniazid
kasA 2518564 c.450C>G synonymous_variant 0.79 isoniazid
kasA 2518567 c.453G>C synonymous_variant 0.85 isoniazid
kasA 2518570 c.456G>C synonymous_variant 0.85 isoniazid
kasA 2518573 c.459G>C synonymous_variant 0.85 isoniazid
kasA 2518574 p.Ile154Val missense_variant 0.85 isoniazid
kasA 2518579 c.465T>C synonymous_variant 0.92 isoniazid
kasA 2518588 c.474T>C synonymous_variant 1.0 isoniazid
kasA 2518591 c.477G>C synonymous_variant 1.0 isoniazid
kasA 2518594 c.480C>T synonymous_variant 1.0 isoniazid
kasA 2518606 c.492G>C synonymous_variant 1.0 isoniazid
kasA 2518609 p.Met165Ile missense_variant 1.0 isoniazid
kasA 2518618 c.504G>C synonymous_variant 1.0 isoniazid
kasA 2518621 c.507G>T synonymous_variant 1.0 isoniazid
kasA 2518624 c.510C>G synonymous_variant 1.0 isoniazid
kasA 2518636 c.522C>T synonymous_variant 1.0 isoniazid
kasA 2518642 c.528A>G synonymous_variant 1.0 isoniazid
kasA 2518672 c.558G>C synonymous_variant 0.9 isoniazid
mtrB 3625729 c.885A>G synonymous_variant 0.82 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625755 p.Ala287Thr missense_variant 0.91 rifampicin Uncertain significance
bedaquiline
mtrB 3625774 c.840G>A synonymous_variant 0.38 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625806 c.808A>C synonymous_variant 0.95 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625819 c.795G>A synonymous_variant 0.95 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625837 c.-927C>T upstream_gene_variant 0.94 rifampicin
bedaquiline
mtrB 3625852 c.762A>G synonymous_variant 0.94 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625864 c.-954T>G upstream_gene_variant 0.94 rifampicin
bedaquiline
mtrB 3625867 c.747A>G synonymous_variant 0.95 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625879 c.735G>A synonymous_variant 0.92 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625899 p.Val239Leu missense_variant 0.93 rifampicin
bedaquiline
lpqB 3625909 c.-999T>G upstream_gene_variant 0.92 rifampicin
bedaquiline
mtrB 3625912 c.702G>A synonymous_variant 0.85 rifampicin
bedaquiline
clpC1 4039073 c.1632C>G synonymous_variant 0.92 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.92 pyrazinamide
clpC1 4039090 c.1615C>T synonymous_variant 0.83 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.92 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.82 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.91 pyrazinamide