TB-Profiler result

Run: ERR234583
Summary

Run ID: ERR234583

Sample name:

Date: 2024-10-03T23:42:21.628759

Number of reads: 6746356

Percentage reads mapped: 99.54

Median coverage: 149.0

Strain: lineage2.2.1;lineage4.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.82
lineage4.2 Euro-American None 0.17
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.82
lineage2.2 East-Asian (Beijing) RD105;RD207 0.83
lineage4 Euro-American None 0.18
lineage4.2.1 Euro-American (TUR) None 0.18
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
isoniazid inhA c.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Tyr41* Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.906A>G Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>T Assoc w R - Interim
capreomycin rrs n.1402C>T Assoc w R
kanamycin rrs n.1402C>T Assoc w R - Interim
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
ethA c.1303delA Assoc w R
c.987_999delAGGTCGCGAACTG 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 761110 p.Asp435Val missense_variant 0.14 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.84 streptomycin Assoc w R
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance Mutation from literature
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 0.16 amikacin Assoc w R - Interim
capreomycin Assoc w R
kanamycin Assoc w R - Interim
inhA 1674048 c.-154G>A upstream_gene_variant 0.13 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289119 p.Tyr41* stop_gained 0.2 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.22 ethambutol Assoc w R
ethA 4326170 c.1303delA frameshift_variant 0.14 ethionamide Assoc w R
ethA 4326474 c.987_999delAGGTCGCGAACTG 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491247 c.465C>T synonymous_variant 0.16 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.82 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.83 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 619969 p.Val27Ile missense_variant 0.15 kanamycin Uncertain significance
capreomycin Not assoc w R - Interim
amikacin Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.84 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.84 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.86 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 0.84 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.78 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.82 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.12 linezolid
Rv1129c 1254477 p.Ala20Thr missense_variant 0.13 levofloxacin
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.87 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.78 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.82 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.76 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 0.15 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.78 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.86 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.2 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726754 p.Gly188Ser missense_variant 0.83 isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.16 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.87 pyrazinamide Not assoc w R - Interim
lpqB 3623222 c.1689A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.83 rifampicin Not assoc w R
bedaquiline Uncertain significance
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 4245187 p.Thr652Lys missense_variant 0.88 ethambutol Uncertain significance
embB 4249594 c.3081G>A synonymous_variant 0.15 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.84 ethambutol Not assoc w R
ethA 4328376 c.-903G>C upstream_gene_variant 0.23 ethionamide
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 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.8 streptomycin Not assoc w R
gid 4407713 p.Gly164Arg missense_variant 0.27 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.82 streptomycin Not assoc w R