TB-Profiler result

Run: SRR25340949
Summary

Run ID: SRR25340949

Sample name:

Date: 2024-04-15T13:25:03.816993

Number of reads: 4122901

Percentage reads mapped: 99.29

Median coverage: 125.0

Strain: lineage1.1.2;lineage3.1.2

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 0.32
lineage1.1.2 Indo-Oceanic RD239 0.76
lineage3.1.2 East-African-Indian RD750 0.43
lineage1.1 Indo-Oceanic RD239 0.68
lineage1 Indo-Oceanic RD239 0.74
lineage3.1 East-African-Indian RD750 0.31
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94His Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94His 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 7581 p.Asp94His missense_variant 0.44 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.24 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.33 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.21 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 5824 c.585A>G synonymous_variant 0.63 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.51 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.51 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 0.61 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.77 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 0.62 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.63 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.99 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.4 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.72 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.66 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.55 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.39 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.6 rifampicin Not assoc w R
rpoB 760850 c.1044G>T synonymous_variant 0.23 rifampicin
rpoB 761349 p.Asp515Tyr missense_variant 0.77 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.36 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 0.6 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.59 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.68 rifampicin Not assoc w R
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 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776107 p.Leu792Val missense_variant 0.29 clofazimine
bedaquiline
mmpL5 776395 p.Phe696Leu missense_variant 0.69 clofazimine Not assoc w R
bedaquiline Uncertain significance
mmpL5 777786 p.Met232Thr missense_variant 0.35 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.68 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 1302962 p.Ala11Val missense_variant 0.74 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.72 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.76 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.74 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475488 n.1831G>A non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
tsnR 1853974 c.369C>T synonymous_variant 0.75 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.84 linezolid Not assoc w R
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 0.76 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 0.5 pyrazinamide Uncertain significance
PPE35 2168604 p.Pro670Leu missense_variant 0.55 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.5 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 0.43 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.38 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.76 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.53 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.52 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.21 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 0.7 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.56 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 3064839 c.1353C>A synonymous_variant 0.57 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066322 c.-131G>A upstream_gene_variant 0.43 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyX 3067945 p.Val1Met missense_variant 0.29 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.65 ethionamide Uncertain significance
lpqB 3623549 c.1362C>T synonymous_variant 0.8 bedaquiline
rifampicin
lpqB 3624486 p.Asp142Gly missense_variant 0.77 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 0.75 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
clpC1 4040149 p.Lys186Glu missense_variant 0.69 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.76 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.76 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.13 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.75 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
glpK 4138622 c.1134C>T synonymous_variant 0.42 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4239593 c.-270G>A upstream_gene_variant 0.73 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.85 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.79 ethambutol Not assoc w R
embC 4241993 p.Ala711Thr missense_variant 0.74 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.27 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 0.76 ethambutol Not assoc w R
embA 4244924 c.1692G>A synonymous_variant 0.22 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.63 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.78 ethambutol Not assoc w R
embB 4249196 p.Gly895Arg missense_variant 0.74 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.65 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.74 ethambutol Not assoc w R
ethA 4326432 p.Leu348Phe missense_variant 0.65 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 0.79 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.99 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.75 streptomycin Not assoc w R