TB-Profiler result

Run: SRR25827496
Summary

Run ID: SRR25827496

Sample name:

Date: 2024-04-15T13:26:02.725548

Number of reads: 5527692

Percentage reads mapped: 97.85

Median coverage: 187.0

Strain: lineage4.1.1.1

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
lineage4.1 Euro-American None 0.87
lineage4.1.1.1 Euro-American (X-type) RD183 0.87
lineage4 Euro-American None 0.93
lineage4.1.1 Euro-American (X-type) None 0.88
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser428Ile Assoc w R - Interim
p.Leu430Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Asn 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 7581 p.Asp94Asn missense_variant 0.92 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761089 p.Ser428Ile missense_variant 0.82 rifampicin Assoc w R - Interim
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin Assoc w R
katG 2155167 p.Ser315Thr missense_variant 0.88 isoniazid Assoc w R High-level resistance
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.87 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.88 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.91 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473371 n.1526C>T non_coding_transcript_exon_variant 0.8 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673368 c.-72A>G upstream_gene_variant 0.86 ethionamide
isoniazid
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
PPE35 2167926 p.Leu896Ser missense_variant 0.17 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726210 c.18T>C synonymous_variant 0.88 isoniazid Not assoc w R - Interim
ribD 2987506 p.Leu223Arg missense_variant 0.17 para-aminosalicylic_acid
Rv2752c 3066470 c.-279G>A upstream_gene_variant 0.88 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641447 p.Thr302Met missense_variant 0.86 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
rpoA 3877553 p.Glu319Lys missense_variant 0.88 rifampicin Not assoc w R
embC 4240897 c.1035C>G synonymous_variant 0.93 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.86 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.22 ethambutol
embB 4247507 p.Trp332Arg missense_variant 0.86 ethambutol Uncertain significance
embB 4249408 c.2895G>A synonymous_variant 0.9 ethambutol Not assoc w R
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