TB-Profiler result

Run: SRR28393997
Summary

Run ID: SRR28393997

Sample name:

Date: 2024-05-22T14:08:58.878891

Number of reads: 8251076

Percentage reads mapped: 99.78

Median coverage: 236.0

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) None 0.78
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.78
lineage4.3.4.2 Euro-American (LAM) RD174 0.77
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Thr400Ala Uncertain significance Mutation from literature
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. 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.Trp119Gly Assoc w R - Interim
p.Ala46Val Assoc w R - Interim
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ser91Pro Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.966_968dupGAC Mutation from literature
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 7572 p.Ser91Pro missense_variant 0.81 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)
rpoB 761004 p.Thr400Ala missense_variant 0.17 rifampicin Uncertain significance Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.74 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 0.28 isoniazid Assoc w R High-level resistance
pncA 2288887 p.Trp119Gly missense_variant 0.23 pyrazinamide Assoc w R - Interim
pncA 2289105 p.Ala46Val missense_variant 0.79 pyrazinamide Assoc w R - Interim
ethA 4326505 c.966_968dupGAC disruptive_inframe_insertion 0.21 ethionamide 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
dnaA 1326 p.Gln442His missense_variant 0.83 isoniazid 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
mshA 575837 c.490C>T synonymous_variant 0.25 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rpoB 761889 p.Val695Leu missense_variant 0.19 rifampicin Uncertain significance
rpoB 761998 p.Leu731Pro missense_variant 0.8 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.8 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777875 c.605delG frameshift_variant 0.22 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpR5 779181 c.198dupG frameshift_variant 0.21 clofazimine Assoc w R
bedaquiline Assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.23 linezolid Not assoc w R - Interim
embR 1417792 c.-445G>C upstream_gene_variant 0.79 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834234 c.693G>A synonymous_variant 0.82 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
ndh 2101831 c.1212G>A synonymous_variant 0.23 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
katG 2156173 c.-62C>A upstream_gene_variant 0.2 isoniazid Uncertain significance
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.15 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726141 c.-52C>A upstream_gene_variant 0.22 isoniazid Uncertain significance
folC 2747481 p.Glu40Lys missense_variant 0.81 para-aminosalicylic_acid
Rv2752c 3065293 p.Val300Ala missense_variant 0.82 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
Rv2752c 3065517 c.675C>T synonymous_variant 0.24 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.78 para-aminosalicylic_acid
thyA 3074495 c.-24C>T upstream_gene_variant 0.23 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.78 cycloserine
ald 3087541 p.Val241Ala missense_variant 0.14 cycloserine
Rv3083 3449722 p.Cys407Arg missense_variant 0.16 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.82 pyrazinamide Not assoc w R
Rv3236c 3612219 p.Val300Ile missense_variant 0.16 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.76 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626633 c.-20G>A upstream_gene_variant 0.76 bedaquiline Uncertain significance
rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.81 pyrazinamide Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.93 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239763 c.-100C>T upstream_gene_variant 0.78 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGC frameshift_variant&missense_variant 0.71 ethambutol
embB 4247884 c.1371C>A synonymous_variant 0.76 ethambutol Not assoc w R - Interim
ethA 4326759 p.Arg239Trp missense_variant 0.78 ethionamide Uncertain significance
ethA 4328317 c.-844C>T upstream_gene_variant 0.2 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407967 p.Leu79Trp missense_variant 0.19 streptomycin Uncertain significance
gid 4408061 p.His48Tyr missense_variant 0.78 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.78 streptomycin Not assoc w R