TB-Profiler result

Run: SRR3103071
Summary

Run ID: SRR3103071

Sample name:

Date: 2024-04-15T17:35:43.561300

Number of reads: 8498052

Percentage reads mapped: 99.2

Median coverage: 170.0

Strain: lineage1.1.2;lineage3

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
lineage3 East-African-Indian RD750 0.15
lineage1.1.2 Indo-Oceanic RD239 0.85
lineage1.1 Indo-Oceanic RD239 0.86
lineage1 Indo-Oceanic RD239 0.87
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gly406Asp Assoc w R
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly 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 7582 p.Asp94Gly missense_variant 0.11 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761109 p.Asp435Tyr missense_variant 0.2 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.82 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.86 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247730 p.Gly406Asp missense_variant 0.91 ethambutol 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
gyrB 6112 p.Met291Ile missense_variant 0.86 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8452 p.Ala384Val missense_variant 0.84 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8948 c.1647G>A synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 0.87 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
Rv0010c 13298 p.Ile87Met missense_variant 0.9 isoniazid Not assoc w R
Rv0010c 13304 c.255G>A synonymous_variant 0.9 isoniazid Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 0.81 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.14 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.86 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.89 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.82 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.18 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.86 rifampicin Not assoc w R
rpoB 760718 c.913_924dupGTCGGTCGCTAT conservative_inframe_insertion 0.77 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 0.13 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.83 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.84 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.85 rifampicin Not assoc w R
rpoC 765844 c.2475C>T synonymous_variant 0.84 rifampicin
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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776395 p.Phe696Leu missense_variant 0.87 clofazimine Not assoc w R
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.84 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303051 p.Val41Met missense_variant 0.83 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.86 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.86 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.83 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.84 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.87 linezolid Not assoc w R
tsnR 1854277 c.672G>A synonymous_variant 0.86 linezolid
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 2062922 p.Ile603Val missense_variant 0.83 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.86 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.88 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223136 p.Ala10Val missense_variant 0.88 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.12 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.16 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.9 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.89 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.11 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.11 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2681 2996912 c.174C>T synonymous_variant 0.89 capreomycin Not assoc w R
Rv2681 2997774 p.Ala346Ser missense_variant 0.18 capreomycin
Rv2752c 3064632 c.1560C>T synonymous_variant 0.85 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv2752c 3064809 c.1383C>T synonymous_variant 0.86 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066271 c.-80A>G upstream_gene_variant 0.82 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.89 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.92 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.93 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.86 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.86 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.16 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.9 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4239593 c.-270G>A upstream_gene_variant 0.81 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.82 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.89 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.13 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.87 ethambutol Not assoc w R
embA 4244167 p.Ala312Val missense_variant 0.88 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.8 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.89 ethambutol Not assoc w R
embB 4249000 c.2487T>G synonymous_variant 0.13 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.87 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.88 ethambutol Not assoc w R
ethA 4326432 p.Leu348Phe missense_variant 0.87 ethionamide 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 4338603 c.-82C>T upstream_gene_variant 0.87 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 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.85 streptomycin Not assoc w R
gid 4407916 p.Arg96Leu missense_variant 0.15 streptomycin Uncertain significance