TB-Profiler result

Run: SRR19428523
Summary

Run ID: SRR19428523

Sample name:

Date: 2024-04-16T08:25:59.226110

Number of reads: 1586104

Percentage reads mapped: 99.69

Median coverage: 85.0

Strain: lineage1.1;lineage2.2;lineage3.1.1;lineage4.2.2.2;lineage4.3.3

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.2
lineage3 East-African-Indian RD750 0.13
lineage4.3 Euro-American (LAM) None 0.45
lineage2 East-Asian RD105 0.08
lineage3.1.1 East-African-Indian RD750 0.17
lineage4.2 Euro-American None 0.16
lineage1.1 Indo-Oceanic RD239 0.08
lineage2.2 East-Asian (Beijing) RD105;RD207 0.09
lineage4 Euro-American None 0.65
lineage1 Indo-Oceanic RD239 0.12
lineage4.3.3 Euro-American (LAM) RD115 0.46
lineage4.2.2.2 Euro-American (Ural) None 0.22
lineage3.1 East-African-Indian RD750 0.17
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 pncA p.Glu111* Assoc w R
streptomycin rpsL p.Lys88Met Assoc w R
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
rpsL 781822 p.Lys88Met missense_variant 0.15 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.13 isoniazid Assoc w R High-level resistance
pncA 2288911 p.Glu111* stop_gained 0.15 pyrazinamide 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 6444 p.Asp402Gly missense_variant 0.38 levofloxacin
moxifloxacin
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 8040 p.Gly247Ser missense_variant 0.45 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8688 p.Ala463Ser missense_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.18 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 0.15 isoniazid Not assoc w R
Rv0010c 13304 c.255G>A synonymous_variant 0.15 isoniazid Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 0.1 isoniazid Not assoc w R
fgd1 490609 c.-174G>C upstream_gene_variant 0.39 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 0.42 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575909 p.Leu188Val missense_variant 0.45 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 576077 c.730C>T synonymous_variant 0.27 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.15 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.42 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.19 ethionamide Uncertain significance
Rv0565c 657425 p.Gly16Ser missense_variant 0.15 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.12 rifampicin Not assoc w R
rpoB 761489 c.1683G>A synonymous_variant 0.14 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.23 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.39 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.35 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.12 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 0.31 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.12 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.11 clofazimine Not assoc w R
bedaquiline Uncertain significance
mmpR5 779111 p.Gly41Val missense_variant 0.25 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.22 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.42 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.15 ethambutol Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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 2063911 p.Ile273Thr missense_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.42 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.29 pyrazinamide Not assoc w R
PPE35 2170461 p.Gly51Glu missense_variant 0.19 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.12 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 0.19 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.13 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.53 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.12 capreomycin Not assoc w R
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.2 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.41 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.19 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.12 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.21 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 0.11 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.13 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.63 pyrazinamide Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.14 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 0.12 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.14 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.11 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.11 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.27 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.1 ethambutol Not assoc w R
ethA 4326432 p.Leu348Phe missense_variant 0.13 ethionamide Uncertain significance
whiB6 4338367 p.Leu52Gln missense_variant 0.49 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
whiB6 4338846 c.-325T>G upstream_gene_variant 0.11 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.4 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.1 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.18 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.13 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.5 streptomycin Not assoc w R