TB-Profiler result

Run: SRR5709818
Summary

Run ID: SRR5709818

Sample name:

Date: 2024-04-14T08:47:06.244808

Number of reads: 1701893

Percentage reads mapped: 99.55

Median coverage: 48.0

Strain: lineage1.2.1.2;lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.2 Indo-Oceanic RD239 0.26
lineage2 East-Asian RD105 0.73
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.76
lineage2.2 East-Asian (Beijing) RD105;RD207 0.75
lineage1 Indo-Oceanic RD239 0.24
lineage1.2.1 Indo-Oceanic RD239 0.22
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.Gly406Asp Assoc w R
pyrazinamide pncA p.Ile31Thr Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.639_640delGT Assoc w R
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 761155 p.Ser450Leu missense_variant 0.65 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.83 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.78 isoniazid Assoc w R High-level resistance
pncA 2289150 p.Ile31Thr missense_variant 0.73 pyrazinamide Assoc w R - Interim
embB 4247730 p.Gly406Asp missense_variant 0.84 ethambutol Assoc w R
ethA 4326833 c.639_640delGT frameshift_variant 0.78 ethionamide 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 8452 p.Ala384Val missense_variant 0.19 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.31 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9260 c.1959G>C synonymous_variant 0.26 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 13175 c.384T>C synonymous_variant 0.32 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.32 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.37 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575368 c.21T>C synonymous_variant 0.32 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.71 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.72 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.69 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.67 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.25 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.26 rifampicin Not assoc w R
rpoB 761998 p.Leu731Pro missense_variant 0.77 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763531 c.162G>C synonymous_variant 0.19 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
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 0.89 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.72 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 0.31 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 1303312 p.Ile128Val missense_variant 0.82 clofazimine
pretomanid
delamanid
Rv1258c 1406760 c.580_581insC frameshift_variant 0.78 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417793 c.-446C>T upstream_gene_variant 0.22 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474732 n.1075A>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.76 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.25 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 0.22 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
Rv1979c 2222308 p.Asp286Gly missense_variant 0.33 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
kasA 2518132 c.18C>T synonymous_variant 0.29 isoniazid
kasA 2519048 p.Gly312Ser missense_variant 0.28 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.26 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.25 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.77 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.16 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 3626562 p.Pro18Ser missense_variant 0.74 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.24 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.22 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
embC 4240671 p.Thr270Ile missense_variant 0.29 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.18 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 0.8 ethambutol Not assoc w R
embA 4243580 c.348G>A synonymous_variant 0.22 ethambutol Not assoc w R
embA 4244420 c.1188G>C synonymous_variant 0.27 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.3 ethambutol Not assoc w R
embB 4247578 c.1065G>A synonymous_variant 0.24 ethambutol Not assoc w R
aftB 4267435 p.Pro468Ser missense_variant 0.75 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.72 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.22 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.16 ethambutol Not assoc w R
whiB6 4338361 p.Arg54Gln missense_variant 0.23 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin 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 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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.2 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.76 streptomycin Not assoc w R