TB-Profiler result

Run: SRR28393273
Summary

Run ID: SRR28393273

Sample name:

Date: 2024-05-22T17:09:26.875968

Number of reads: 9218444

Percentage reads mapped: 99.57

Median coverage: 233.0

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 0.29
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.28
lineage4.3.4.2 Euro-American (LAM) RD174 0.26
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Arg Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide
streptomycin
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.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.397_398dupCG Assoc w R
kanamycin
cycloserine
ethionamide ethA c.757delT Assoc w R
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 0.77 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
gyrA 7582 p.Asp94Ala missense_variant 0.21 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761140 p.His445Arg missense_variant 0.71 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.29 rifampicin Assoc w R
tlyA 1918334 c.397_398dupCG frameshift_variant 0.52 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.69 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.27 ethambutol Assoc w R
ethA 4326716 c.757delT frameshift_variant 0.3 ethionamide 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
gyrB 6931 c.1692A>G synonymous_variant 0.79 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.99 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
rpoB 759590 c.-217A>C upstream_gene_variant 0.76 rifampicin Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 0.27 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.27 rifampicin Not assoc w R
rpoC 766446 p.Gly1026Val missense_variant 0.74 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 775978 p.Val835Met missense_variant 0.74 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254588 c.-54T>G upstream_gene_variant 0.25 moxifloxacin
levofloxacin
rifampicin
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475780 n.2123A>G non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.99 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155017 c.1095G>A synonymous_variant 0.26 isoniazid Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2747453 p.Arg49Gln missense_variant 0.27 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.22 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3449122 c.620delT frameshift_variant 0.66 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.3 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840259 p.Tyr388Asp missense_variant 0.69 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.65 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242147 p.Asn762Ser missense_variant 0.74 ethambutol Uncertain significance
embC 4242377 p.Leu839Met missense_variant 0.63 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4327445 p.Val10Gly missense_variant 0.74 ethionamide Uncertain significance
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 4338600 c.-79T>C upstream_gene_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 0.99 capreomycin
amikacin
kanamycin
gid 4407989 p.Ala72Thr missense_variant 0.79 streptomycin Uncertain significance
gid 4408054 p.Leu50Arg missense_variant 0.22 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.23 streptomycin Not assoc w R