TB-Profiler result

Run: SRR25827511
Summary

Run ID: SRR25827511

Sample name:

Date: 2024-10-04T22:37:09.358543

Number of reads: 8346451

Percentage reads mapped: 99.17

Median coverage: 258.0

Strain: lineage2.2.1;lineage3.1.2;lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.79
lineage3.1.2 East-African-Indian RD750 0.77
lineage2 East-Asian RD105 0.07
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.09
lineage4 Euro-American None 0.08
lineage4.9 Euro-American (H37Rv-like) None 0.06
lineage3.1 East-African-Indian RD750 0.74
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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
katG 2155168 p.Ser315Thr missense_variant 0.14 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 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.92 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.91 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.83 rifampicin Not assoc w R
rpoB 761231 c.1425C>T synonymous_variant 0.76 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.82 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.93 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.95 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.93 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.93 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.92 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406242 p.Ala367Thr missense_variant 0.7 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.95 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.95 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.93 capreomycin Not assoc w R
tlyA 1918104 c.165G>A synonymous_variant 0.81 capreomycin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.92 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.94 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.77 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.94 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.79 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.74 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.84 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.79 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.92 cycloserine
whiB7 3568425 c.255T>G synonymous_variant 0.14 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.13 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.94 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.84 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.74 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.78 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.96 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.19 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 0.93 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.91 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.96 streptomycin Not assoc w R