TB-Profiler result

Run: SRR15368794
Summary

Run ID: SRR15368794

Sample name:

Date: 2024-10-05T09:00:35.211998

Number of reads: 7524020

Percentage reads mapped: 99.59

Median coverage: 231.0

Strain: lineage4.4.2;lineage4.5

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.25
lineage4 Euro-American None 1.0
lineage4.4 Euro-American None 0.56
lineage4.4.2 Euro-American None 0.59
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
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 7892 c.591G>A synonymous_variant 0.28 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8147 p.Asn282Lys missense_variant 0.13 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576690 p.Tyr448Cys missense_variant 0.19 isoniazid
ethionamide
ccsA 620029 c.139C>T synonymous_variant 0.26 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
rplC 801273 c.465C>G synonymous_variant 0.64 linezolid
fbiC 1304501 p.Ala524Gly missense_variant 0.13 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fbiC 1305357 c.2427C>G synonymous_variant 0.19 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471850 n.5G>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rpsA 1834803 p.Ala421Val missense_variant 0.21 pyrazinamide
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
bacA 2062923 c.1806G>A synonymous_variant 0.32 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2168742 p.Gly624Asp missense_variant 0.17 pyrazinamide Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.26 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
eis 2714211 c.1122G>A synonymous_variant 0.23 kanamycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
folC 2747788 c.-190C>T upstream_gene_variant 0.19 para-aminosalicylic_acid
Rv2752c 3066099 p.Met31Ile missense_variant 0.66 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.6 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 0.24 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.27 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.51 ethambutol Not assoc w R
embC 4242182 p.Ala774Thr missense_variant 0.58 ethambutol
embC 4242397 c.2535G>A synonymous_variant 0.24 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243817 p.Phe195Leu missense_variant 0.19 ethambutol
embA 4246508 c.3276G>A synonymous_variant 0.6 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.53 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.58 ethambutol Not assoc w R
ethA 4326009 p.Val489Phe missense_variant 0.28 ethionamide Uncertain significance
ethA 4327376 p.Ala33Gly missense_variant 0.19 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 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
whiB6 4338839 c.-318T>C upstream_gene_variant 0.25 kanamycin
capreomycin
amikacin