TB-Profiler result

Run: SRR25827856
Summary

Run ID: SRR25827856

Sample name:

Date: 2024-03-26T22:11:01.540253

Number of reads: 8468230

Percentage reads mapped: 92.37

Median coverage: 272.0

Strain: lineage2.2.1;lineage3

Spoligotype:

Drug-resistance: MDR-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 0.54
lineage2 East-Asian RD105 0.44
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.46
lineage2.2 East-Asian (Beijing) RD105;RD207 0.45
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gly406Ser Assoc w R
pyrazinamide pncA p.Leu159Arg Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.198dupG 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
rpoB 761110 p.Asp435Val missense_variant 0.21 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.76 rifampicin Assoc w R
mmpR5 779181 c.198dupG frameshift_variant 0.36 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 0.36 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.41 isoniazid Assoc w R High-level resistance
pncA 2288766 p.Leu159Arg missense_variant 0.46 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.41 ethambutol Assoc w R
embB 4247729 p.Gly406Ser missense_variant 0.53 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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.53 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 0.42 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.42 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.48 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.63 rifampicin Not assoc w R
rpoB 760361 c.555T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760370 c.564C>G synonymous_variant 0.16 rifampicin
rpoB 760376 p.Asp190Glu missense_variant 0.16 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.63 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763040 c.3234C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
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 0.35 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.43 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800612 c.-197A>G upstream_gene_variant 0.16 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.16 linezolid
rplC 800648 c.-161A>T upstream_gene_variant 0.18 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.16 linezolid
rplC 800693 c.-116A>G upstream_gene_variant 0.16 linezolid
rplC 800703 c.-106T>C upstream_gene_variant 0.16 linezolid
Rv1129c 1253930 p.Phe202Tyr missense_variant 0.48 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
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
Rv1258c 1406760 c.580_581insC frameshift_variant 0.42 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.19 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1474960 n.1303C>G non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rpsA 1834000 c.459G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.56 pyrazinamide Not assoc w R - Interim
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
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
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 0.58 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.49 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.52 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.53 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
pepQ 2860448 c.-30C>A upstream_gene_variant 0.56 clofazimine
bedaquiline
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087756 p.Leu313Met missense_variant 0.5 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.38 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.44 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878416 p.Gly31Ala missense_variant 0.41 rifampicin Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.55 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.5 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 4241022 p.Ala387Val missense_variant 0.43 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.52 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 0.49 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.17 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.33 ethambutol Not assoc w R
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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.44 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.38 streptomycin Not assoc w R