TB-Profiler result

Run: SRR1049975
Summary

Run ID: SRR1049975

Sample name:

Date: 2024-10-05T12:55:58.834735

Number of reads: 8100578

Percentage reads mapped: 98.7

Median coverage: 172.0

Strain: lineage4.1.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.83
lineage4.1 Euro-American None 1.0
lineage4 Euro-American 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.Asp435Glu Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Ser441Leu 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
pyrazinamide pncA p.Val139Ala 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 761111 p.Asp435Glu missense_variant 0.82 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761128 p.Ser441Leu missense_variant 0.8 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.8 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 0.85 isoniazid Assoc w R High-level resistance
pncA 2288826 p.Val139Ala missense_variant 0.87 pyrazinamide Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.84 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
gyrB 6507 p.Ala423Val missense_variant 0.18 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9557 c.2256G>C synonymous_variant 0.88 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9656 c.2355C>G synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765187 c.1818C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766012 c.2643C>G synonymous_variant 0.1 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775973 p.Leu836Phe missense_variant 0.17 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776411 c.2070T>C synonymous_variant 0.16 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpL5 776750 c.1731C>T synonymous_variant 0.15 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781421 c.-139C>A upstream_gene_variant 1.0 streptomycin Uncertain significance
fbiC 1304610 c.1680C>T synonymous_variant 0.84 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rrs 1471627 n.-219C>T upstream_gene_variant 0.21 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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
katG 2156007 c.105C>T synonymous_variant 0.12 isoniazid Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623291 c.1620C>A synonymous_variant 0.77 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
lpqB 3624660 p.Ala84Gly missense_variant 0.8 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627293 c.57G>A synonymous_variant 0.18 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
alr 3840288 p.Asp378Gly missense_variant 0.15 cycloserine
rpoA 3878652 c.-145C>T upstream_gene_variant 0.17 rifampicin Uncertain significance
clpC1 4039835 c.870C>T synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
panD 4044479 c.-198C>T upstream_gene_variant 0.13 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
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