TB-Profiler result

Run: SRR998803
Summary

Run ID: SRR998803

Sample name:

Date: 2024-10-04T21:08:26.194246

Number of reads: 3613978

Percentage reads mapped: 99.34

Median coverage: 82.0

Strain: lineage4.1.3;lineage5.1.1

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.89
lineage4.1 Euro-American None 0.88
lineage4 Euro-American None 0.9
lineage5.1.1 West-Africa 1 RD711 0.08
lineage5 West-Africa 1 RD711 0.08
lineage5.1 West-Africa 1 RD711 0.07
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asp Assoc w R
isoniazid inhA c.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Ile133Thr Assoc w R
streptomycin gid p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
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 761139 p.His445Asp missense_variant 0.9 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.82 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.8 isoniazid Assoc w R High-level resistance
pncA 2288844 p.Ile133Thr missense_variant 0.84 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.92 ethambutol Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.94 streptomycin 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 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9557 c.2256G>C synonymous_variant 0.94 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 0.16 isoniazid Not assoc w R
mshA 574557 c.-791C>G upstream_gene_variant 0.85 isoniazid
ethionamide
Rv0565c 657269 p.Ser68Pro missense_variant 0.85 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.11 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.85 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781421 c.-139C>A upstream_gene_variant 0.86 streptomycin Uncertain significance
fbiC 1304610 c.1680C>T synonymous_variant 0.86 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv1258c 1407273 p.Asp23Val missense_variant 0.15 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.11 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673338 c.-864G>A upstream_gene_variant 0.12 isoniazid
ethionamide
tsnR 1853565 c.-41G>A upstream_gene_variant 0.11 linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.12 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2101921 c.1122G>A synonymous_variant 0.17 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.12 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.14 isoniazid
eis 2715511 c.-179C>T upstream_gene_variant 0.92 kanamycin
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 0.92 cycloserine
lpqB 3623291 c.1620C>A synonymous_variant 0.95 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
lpqB 3624660 p.Ala84Gly missense_variant 0.84 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040010 p.Ala232Asp missense_variant 0.17 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4239843 c.-20A>C upstream_gene_variant 0.15 ethambutol Not assoc w R - Interim
embC 4240986 p.Arg375Gln missense_variant 0.96 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.91 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.12 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.12 ethambutol Not assoc w R
ethA 4326928 c.546C>T synonymous_variant 0.15 ethionamide Not assoc w R - Interim
ethA 4327103 p.Gly124Asp missense_variant 0.13 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.12 streptomycin Not assoc w R