TB-Profiler result

Run: SRR25827340
Summary

Run ID: SRR25827340

Sample name:

Date: 2024-04-16T11:40:36.216149

Number of reads: 40107792

Percentage reads mapped: 96.96

Median coverage: 35.0

Strain: lineage4.1.2.1;lineage4.8

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 0.51
lineage4.1.2 Euro-American None 0.6
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.52
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.38
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
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Tyr34* Assoc w R
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)
ofloxacin
levofloxacin gyrA p.Ala90Val 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 0.63 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289140 p.Tyr34* stop_gained 0.33 pyrazinamide 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 0.57 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.56 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.67 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.48 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.53 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.43 rifampicin Not assoc w R
rpoB 762675 p.Leu957Val missense_variant 0.36 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.6 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 778981 c.-501C>T upstream_gene_variant 0.61 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.53 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
Rv1979c 2223491 c.-327C>A upstream_gene_variant 0.5 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518076 c.-39C>T upstream_gene_variant 0.48 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.59 cycloserine
Rv3083 3448560 c.57G>A synonymous_variant 0.95 ethionamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.56 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626125 c.489C>A synonymous_variant 0.6 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
alr 3841609 c.-190_-189insAAGC upstream_gene_variant 0.38 cycloserine
embC 4239298 c.-565C>T upstream_gene_variant 0.61 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 0.58 ethambutol Not assoc w R
whiB6 4338521 p.Met1? start_lost 0.55 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 4338732 c.-211C>T upstream_gene_variant 0.66 capreomycin
amikacin
kanamycin
gid 4407652 p.Val184Gly missense_variant 0.39 streptomycin