TB-Profiler result

Run: SRR25827550
Summary

Run ID: SRR25827550

Sample name:

Date: 2024-04-14T18:08:12.749398

Number of reads: 8791575

Percentage reads mapped: 99.2

Median coverage: 302.0

Strain: lineage1.1.2;lineage2.2.1;lineage3.1

Spoligotype:

Drug-resistance: 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 0.27
lineage1.1.2 Indo-Oceanic RD239 0.32
lineage2 East-Asian RD105 0.41
lineage1.1 Indo-Oceanic RD239 0.34
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.4
lineage2.2 East-Asian (Beijing) RD105;RD207 0.39
lineage1 Indo-Oceanic RD239 0.31
lineage3.1 East-African-Indian RD750 0.23
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 embA c.-16C>T Uncertain significance Mutation from literature
embB p.Gln497Lys Assoc w R
pyrazinamide pncA p.Ile5Ser Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.583_585delTATinsCG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ser91Pro Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide
clofazimine mmpR5 p.Tyr157* Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid thyA p.Thr22Ala Mutation from literature
delamanid
bedaquiline mmpR5 p.Tyr157* Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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 7572 p.Ser91Pro missense_variant 0.23 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
gyrA 7582 p.Asp94Gly missense_variant 0.42 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761109 p.Asp435Tyr missense_variant 0.24 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.42 rifampicin Assoc w R
mmpR5 779460 p.Tyr157* stop_gained 0.15 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 0.34 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.66 isoniazid Assoc w R High-level resistance
pncA 2289228 p.Ile5Ser missense_variant 0.42 pyrazinamide Assoc w R
eis 2715342 c.-10G>A upstream_gene_variant 0.42 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
thyA 3074408 p.Thr22Ala missense_variant 0.39 para-aminosalicylic_acid Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.38 ethambutol Uncertain significance Mutation from literature
embB 4248002 p.Gln497Lys missense_variant 0.27 ethambutol Assoc w R
gid 4407618 c.583_585delTATinsCG frameshift_variant&missense_variant 0.23 streptomycin 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 0.3 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.32 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 0.35 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.35 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 0.34 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.28 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.36 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.41 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.41 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.65 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.36 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.36 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.28 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.33 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.28 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.29 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.29 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 0.34 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.33 rifampicin Not assoc w R
rpoC 764703 p.Lys445Arg missense_variant 0.42 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.29 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.36 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.33 clofazimine Not assoc w R
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.44 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 0.38 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
sigE 1364397 c.-16C>T upstream_gene_variant 0.35 pyrazinamide Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.42 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.35 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.32 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.3 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476685 n.3028A>T non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 0.28 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.32 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.34 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 0.33 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
katG 2156123 c.-12G>T upstream_gene_variant 0.27 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.99 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.36 pyrazinamide Uncertain significance
PPE35 2170173 p.Asp147Ala missense_variant 0.38 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.27 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 0.3 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.25 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.39 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.29 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.3 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.3 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 2784573 c.-531C>T upstream_gene_variant 0.29 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ribD 2987538 p.Val234Met missense_variant 0.25 para-aminosalicylic_acid
Rv2681 2996912 c.174C>T synonymous_variant 0.37 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.34 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
thyX 3067949 c.-4C>T upstream_gene_variant 0.47 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.32 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.4 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.32 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 0.32 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.4 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040178 p.Arg176His missense_variant 0.24 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.4 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.34 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.28 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.32 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 0.26 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 4240671 p.Thr270Ile missense_variant 0.3 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.4 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.35 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.24 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243225 c.-8C>T upstream_gene_variant 0.26 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.39 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.33 ethambutol Not assoc w R
embA 4245218 c.1986C>T synonymous_variant 0.34 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.3 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.17 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.33 ethambutol Not assoc w R
embB 4247847 p.Gln445Arg missense_variant 0.42 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.45 ethambutol Not assoc w R
ubiA 4269031 p.Gly268Asp missense_variant 0.38 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.35 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.31 ethambutol Not assoc w R
ethA 4327060 p.Ser138Arg missense_variant 0.41 ethionamide Uncertain significance
whiB6 4338354 p.Cys56* stop_gained 0.29 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338397 p.Thr42Met missense_variant 0.18 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 0.97 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.31 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 0.37 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.37 streptomycin Not assoc w R