TB-Profiler result

Run: SRR4037761
Summary

Run ID: SRR4037761

Sample name:

Date: 2024-03-26T17:15:48.724362

Number of reads: 5795718

Percentage reads mapped: 99.63

Median coverage: 112.0

Strain: lineage2.2.1;lineage4.4.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.15
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.1
lineage2.2 East-Asian (Beijing) RD105;RD207 0.13
lineage4.4.1 Euro-American (S-type) None 0.89
lineage4 Euro-American None 0.89
lineage4.4.1.1 Euro-American None 0.9
lineage4.4 Euro-American None 0.89
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 9138 p.Gln613Glu missense_variant 0.96 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
fgd1 491742 c.960T>C synonymous_variant 0.2 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.11 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.16 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.15 ethionamide Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.14 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777416 c.1065G>T synonymous_variant 0.92 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.12 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.12 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476704 n.3053dupC non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
fabG1 1673363 c.-77G>A upstream_gene_variant 0.86 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
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
ndh 2102990 p.Val18Ala missense_variant 0.88 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.13 pyrazinamide Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 0.85 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.87 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
Rv2752c 3066175 p.Pro6Arg missense_variant 0.79 ethambutol Uncertain significance
moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.88 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.92 streptomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.88 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.18 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.86 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 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
gid 4407588 c.615A>G synonymous_variant 0.14 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.14 streptomycin Not assoc w R