TB-Profiler result

Run: SRR25827341
Summary

Run ID: SRR25827341

Sample name:

Date: 2024-10-03T21:22:27.368444

Number of reads: 39603949

Percentage reads mapped: 99.62

Median coverage: 1082.0

Strain: lineage3.1.2;lineage4.3.3

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.28
lineage4.3 Euro-American (LAM) None 0.72
lineage3.1.2 East-African-Indian RD750 0.29
lineage4 Euro-American None 0.72
lineage4.3.3 Euro-American (LAM) RD115 0.72
lineage3.1 East-African-Indian RD750 0.29
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
p.Ser493Leu Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Trp68Arg Assoc w R
c.-10T>C Uncertain significance Mutation from literature
streptomycin gid c.115delC Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.7 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.3 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.26 rifampicin Assoc w R
rpoB 761284 p.Ser493Leu missense_variant 0.72 rifampicin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289040 p.Trp68Arg missense_variant 0.34 pyrazinamide Assoc w R
pncA 2289251 c.-10T>C upstream_gene_variant 0.7 pyrazinamide Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.71 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.28 ethambutol Assoc w R
gid 4408087 c.115delC frameshift_variant 0.25 streptomycin Assoc w R
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 8040 p.Gly247Ser missense_variant 0.69 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
fgd1 491742 c.960T>C synonymous_variant 0.25 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.24 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.29 rifampicin Not assoc w R
rpoB 760321 p.Gln172Arg missense_variant 0.7 rifampicin Uncertain significance
rpoB 761032 p.Gln409Arg missense_variant 0.71 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.26 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.32 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.69 rifampicin Not assoc w R
rpoC 765463 p.Asn698Lys missense_variant 0.3 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.31 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.31 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673406 c.-796C>T upstream_gene_variant 0.68 isoniazid Uncertain significance
ethionamide Uncertain significance
rpsA 1834334 p.Val265Phe missense_variant 0.29 pyrazinamide
rpsA 1834836 p.Met432Thr missense_variant 0.71 pyrazinamide Not assoc w R - Interim
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
tlyA 1918104 c.165G>A synonymous_variant 0.31 capreomycin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.31 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.74 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.27 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.28 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
pncA 2289047 c.195C>T synonymous_variant 0.34 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.29 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.75 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.33 isoniazid Not assoc w R
folC 2746340 p.Ala420Val missense_variant 0.71 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.31 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2477c 2784613 c.-571T>C upstream_gene_variant 0.77 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyA 3073868 p.Thr202Ala missense_variant 0.69 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.73 pyrazinamide Not assoc w R
clpC1 4040323 p.Gly128Ser missense_variant 0.31 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.28 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.27 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.29 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.15 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.15 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.11 ethambutol
embB 4246563 p.Leu17Trp missense_variant 0.14 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.11 ethambutol Not assoc w R - Interim
embB 4247028 p.Leu172Arg missense_variant 0.17 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.14 ethambutol
ethA 4327073 p.Leu134Arg missense_variant 0.28 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 0.22 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 0.3 streptomycin Not assoc w R
gid 4408085 p.Glu40Gln missense_variant 0.75 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.71 streptomycin Not assoc w R