TB-Profiler result

Run: SRR25827351
Summary

Run ID: SRR25827351

Sample name:

Date: 2024-10-03T21:16:21.129994

Number of reads: 3960404

Percentage reads mapped: 49.85

Median coverage: 110.0

Strain: lineage2.2.1;lineage4.1.1.3

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.27
lineage4.1 Euro-American None 0.7
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.29
lineage4.1.1.3 Euro-American (X-type) RD193 0.74
lineage2.2 East-Asian (Beijing) RD105;RD207 0.29
lineage4 Euro-American None 0.72
lineage4.1.1 Euro-American (X-type) None 0.7
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
rpoC p.Ile491Thr Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
pyrazinamide pncA p.Ile5Ser Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
eis c.-12C>T Assoc w R
cycloserine
ethionamide ethA c.1290delC Assoc w R
clofazimine
para-aminosalicylic_acid thyA p.Thr22Ala Mutation from literature
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoC 764841 p.Ile491Thr missense_variant 0.26 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.29 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.73 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 2289228 p.Ile5Ser missense_variant 0.28 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.32 kanamycin Assoc w R
thyA 3074408 p.Thr22Ala missense_variant 0.3 para-aminosalicylic_acid Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.29 ethambutol Uncertain significance Mutation from literature
ethA 4326183 c.1290delC frameshift_variant 0.2 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 491290 p.Val170Met missense_variant 0.3 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.26 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.27 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.27 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.22 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.24 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.65 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.31 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.75 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 0.34 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.28 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.29 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.71 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.28 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 0.26 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 0.33 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
tlyA 1918478 p.Leu180Arg missense_variant 0.29 capreomycin Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.3 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.24 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
thyX 3067949 c.-4C>T upstream_gene_variant 0.29 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.23 pyrazinamide 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 0.28 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840423 p.Arg333Lys missense_variant 0.71 cycloserine
embC 4241022 p.Ala387Val missense_variant 0.26 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.71 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.31 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.28 ethambutol
embB 4247847 p.Gln445Arg missense_variant 0.23 ethambutol Uncertain significance
embB 4249408 c.2895G>A synonymous_variant 0.75 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.22 ethambutol Not assoc w R
whiB6 4338292 p.Ala77Val missense_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 0.24 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.24 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.32 streptomycin Not assoc w R