TB-Profiler result

Run: SRR14802152
Summary

Run ID: SRR14802152

Sample name:

Date: 2024-10-05T04:59:52.563567

Number of reads: 5567062

Percentage reads mapped: 99.46

Median coverage: 165.0

Strain: lineage2.2.1;lineage4.3.3;lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.17
lineage2 East-Asian RD105 0.63
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.67
lineage2.2 East-Asian (Beijing) RD105;RD207 0.64
lineage4 Euro-American None 0.38
lineage4.8 Euro-American (mainly T) RD219 0.17
lineage4.3.3 Euro-American (LAM) RD115 0.16
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.Asn296His Uncertain significance Mutation from literature
pyrazinamide pncA p.Gly105Val Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.46dupC Assoc w R
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide ethA c.110delA 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 0.73 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.6 streptomycin Assoc w R
tlyA 1917983 c.46dupC frameshift_variant 0.62 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.61 isoniazid Assoc w R High-level resistance
pncA 2288928 p.Gly105Val missense_variant 0.68 pyrazinamide Assoc w R - Interim
eis 2715342 c.-10G>A upstream_gene_variant 0.62 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
embB 4247399 p.Asn296His missense_variant 0.61 ethambutol Uncertain significance Mutation from literature
ethA 4327363 c.110delA frameshift_variant 0.63 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 0.83 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.22 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.84 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.66 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.73 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.25 isoniazid
ethionamide
ccsA 620625 p.Ile245Met missense_variant 0.64 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.61 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.58 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.64 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.59 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.2 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.67 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.72 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.65 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.66 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.58 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.57 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.17 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.76 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 0.65 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.2 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.65 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.15 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.19 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.23 para-aminosalicylic_acid
pepQ 2859634 p.Gln262Arg missense_variant 0.16 bedaquiline Uncertain significance
clofazimine Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.16 para-aminosalicylic_acid
ald 3086731 c.-89A>G upstream_gene_variant 0.61 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.82 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.6 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.83 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.61 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.13 pyrazinamide Not assoc w R
clpC1 4038723 p.Val661Ala missense_variant 0.63 pyrazinamide
clpC1 4038968 c.1737G>A synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.6 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.59 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.59 ethambutol Not assoc w R
aftB 4267663 p.Ser392Ala missense_variant 0.14 ethambutol
whiB6 4338371 p.Thr51Pro missense_variant 0.56 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.89 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.69 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.61 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.14 streptomycin Not assoc w R