TB-Profiler result

Run: SRR18715377
Summary

Run ID: SRR18715377

Sample name:

Date: 2024-10-03T16:22:45.564700

Number of reads: 3672362

Percentage reads mapped: 99.67

Median coverage: 100.0

Strain: lineage4.1.2.1;lineage4.8

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.1
lineage4.1.2 Euro-American None 0.11
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.14
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.86
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 gid p.Leu79Ser Uncertain significance Mutation from literature
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
gid 4407967 p.Leu79Ser missense_variant 0.88 streptomycin Uncertain significance 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13262 c.297G>A synonymous_variant 0.87 isoniazid
Rv0010c 13649 c.-91G>T upstream_gene_variant 0.86 isoniazid Uncertain significance
fgd1 490829 p.Ala16Val missense_variant 0.85 pretomanid
delamanid
clofazimine
mshA 575679 p.Asn111Ser missense_variant 0.14 isoniazid Not assoc w R
ethionamide Not assoc w R
mmaA3 737324 p.Ala276Thr missense_variant 0.82 isoniazid
rpoC 765150 p.Gly594Glu missense_variant 0.12 rifampicin Not assoc w R
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.82 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.19 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.94 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.12 isoniazid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.9 capreomycin
mtrB 3625065 p.Met517Leu missense_variant 0.21 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.14 ethambutol Not assoc w R
aftB 4269546 c.-710G>C upstream_gene_variant 0.9 ethambutol
ubiA 4269864 c.-31C>T upstream_gene_variant 0.83 ethambutol 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 0.13 kanamycin
capreomycin
amikacin