TB-Profiler result

Run: SRR19428529
Summary

Run ID: SRR19428529

Sample name:

Date: 2024-04-16T05:58:48.844740

Number of reads: 1474028

Percentage reads mapped: 99.51

Median coverage: 73.5

Strain: lineage1.1.2;lineage3.1.1;lineage4.2.2.2

Spoligotype:

Drug-resistance: MDR-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 0.33
lineage3 East-African-Indian RD750 0.31
lineage1.1.2 Indo-Oceanic RD239 0.22
lineage3.1.1 East-African-Indian RD750 0.31
lineage4.2 Euro-American None 0.37
lineage1.1 Indo-Oceanic RD239 0.24
lineage4 Euro-American None 0.37
lineage1 Indo-Oceanic RD239 0.24
lineage4.2.2.2 Euro-American (Ural) None 0.39
lineage3.1 East-African-Indian RD750 0.36
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Glu Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
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
rpoB 761100 p.Gln432Glu missense_variant 0.3 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpsL 781822 p.Lys88Met missense_variant 0.4 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.33 isoniazid Assoc w R High-level resistance
pncA 2288911 p.Glu111* stop_gained 0.34 pyrazinamide Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.27 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 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.15 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 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8688 p.Ala463Ser missense_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.2 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 0.32 isoniazid Not assoc w R
Rv0010c 13304 c.255G>A synonymous_variant 0.13 isoniazid Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 0.3 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.54 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576077 c.730C>T synonymous_variant 0.4 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.48 ethionamide Not assoc w R - Interim
Rv0565c 657425 p.Gly16Ser missense_variant 0.36 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.33 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.19 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.1 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.31 rifampicin Not assoc w R
rpoB 761248 p.Glu481Ala missense_variant 0.35 rifampicin Uncertain significance
rpoB 761489 c.1683G>A synonymous_variant 0.33 rifampicin Not assoc w R
rpoB 762201 p.Lys799Gln missense_variant 0.13 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.33 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.62 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.21 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.21 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.15 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 0.53 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpR5 779303 p.Arg105His missense_variant 0.21 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 0.39 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.18 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.73 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 0.17 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1406349 p.Ile331Ser missense_variant 0.1 streptomycin
isoniazid
pyrazinamide
embR 1417019 p.Cys110Tyr missense_variant 0.22 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.28 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.2 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.43 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.3 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 0.2 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.37 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.5 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.73 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.25 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.17 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223136 p.Ala10Val missense_variant 0.15 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 0.2 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.32 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.28 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.18 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.27 isoniazid Not assoc w R
ahpC 2726534 c.342C>T synonymous_variant 0.11 isoniazid
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
Rv2477c 2782508 p.Trp512Ser missense_variant 0.21 ethambutol Uncertain significance
moxifloxacin
streptomycin Uncertain significance
levofloxacin
kanamycin
rifampicin Uncertain significance
amikacin
Rv2681 2996912 c.174C>T synonymous_variant 0.16 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.37 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 3066280 c.-89C>T upstream_gene_variant 0.35 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.53 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.17 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.32 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.12 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.29 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.28 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 0.28 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 0.14 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.11 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.22 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.24 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.36 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 0.32 ethambutol Not assoc w R
embA 4244167 p.Ala312Val missense_variant 0.22 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.2 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.26 ethambutol Not assoc w R
embB 4249673 p.Ser1054Pro missense_variant 0.13 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.12 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.31 ethambutol Not assoc w R
ubiA 4269469 p.Pro122Gln missense_variant 0.12 ethambutol Uncertain significance
ubiA 4269606 c.228T>C synonymous_variant 0.29 ethambutol Not assoc w R
ethA 4326432 p.Leu348Phe missense_variant 0.17 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 0.26 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 0.28 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.76 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.13 streptomycin Not assoc w R