TB-Profiler result

Run: SRR25827562
Summary

Run ID: SRR25827562

Sample name:

Date: 2024-04-16T06:42:01.790418

Number of reads: 9493849

Percentage reads mapped: 99.04

Median coverage: 280.0

Strain: lineage2.2.1;lineage4.2.2.2

Spoligotype:

Drug-resistance: XDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.18
lineage2 East-Asian RD105 0.82
lineage4.2 Euro-American None 0.18
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.83
lineage2.2 East-Asian (Beijing) RD105;RD207 0.82
lineage4 Euro-American None 0.16
lineage4.2.2.2 Euro-American (Ural) None 0.19
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
p.Ile480Val Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Arg446His Uncertain significance Mutation from literature
ofloxacin
levofloxacin gyrB p.Arg446His Uncertain significance Mutation from literature
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline atpE p.Ala63Pro Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
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
gyrB 6576 p.Arg446His missense_variant 0.73 moxifloxacin Uncertain significance Mutation from literature
levofloxacin Uncertain significance Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoB 761244 p.Ile480Val missense_variant 0.18 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
atpE 1461231 p.Ala63Pro missense_variant 0.91 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.8 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289162 p.Leu27Pro missense_variant 0.83 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.85 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 491742 c.960T>C synonymous_variant 0.82 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576077 c.730C>T synonymous_variant 0.21 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
mshA 576453 p.Val369Gly missense_variant 0.23 ethionamide
isoniazid
mshA 576651 p.Asp435Ala missense_variant 0.19 ethionamide
isoniazid
ccsA 620625 p.Ile245Met missense_variant 0.84 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.82 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.85 ethionamide Uncertain significance
Rv0565c 657425 p.Gly16Ser missense_variant 0.22 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.88 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_variant 0.85 rifampicin Uncertain significance
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 0.79 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.88 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 0.2 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.8 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 0.85 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.79 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
bacA 2063911 p.Ile273Thr missense_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.79 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.75 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
ribD 2986827 c.-12G>A upstream_gene_variant 0.19 para-aminosalicylic_acid
Rv2752c 3065298 c.894C>T synonymous_variant 0.81 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.19 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3569220 c.-541C>T upstream_gene_variant 0.8 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.82 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.8 bedaquiline Uncertain significance
rifampicin 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 4245835 p.Leu868Arg missense_variant 0.17 ethambutol
embB 4247015 p.Ser168Ala missense_variant 0.22 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.71 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.81 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.91 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.85 streptomycin Not assoc w R