TB-Profiler result

Run: SRR25827439
Summary

Run ID: SRR25827439

Sample name:

Date: 2024-10-04T21:19:12.538364

Number of reads: 5160101

Percentage reads mapped: 98.01

Median coverage: 169.0

Strain: lineage2.2.1.2;lineage3.1.2.1

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.65
lineage3.1.2 East-African-Indian RD750 0.41
lineage2 East-Asian RD105 0.38
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.33
lineage2.2 East-Asian (Beijing) RD105;RD207 0.34
lineage2.2.1.2 East-Asian (Beijing) RD105;RD207;RD181;RD142 0.34
lineage3.1.2.1 East-African-Indian RD750 0.34
lineage3.1 East-African-Indian RD750 0.3
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
p.Ser450Leu Assoc w R
rpoC p.Leu527Val Uncertain significance Mutation from literature
isoniazid inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. 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
p.Met306Ile Assoc w R
pyrazinamide pncA p.Ala171Val Uncertain significance Mutation from literature
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.87delC Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
ethA p.Tyr408* Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid rrl n.2814G>T Assoc w R - Interim
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 7570 p.Ala90Val missense_variant 0.19 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Ala missense_variant 0.56 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761095 p.Leu430Pro missense_variant 0.23 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.73 rifampicin Assoc w R
rpoC 764948 p.Leu527Val missense_variant 0.51 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.53 streptomycin Assoc w R
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.19 linezolid Assoc w R - Interim
inhA 1673432 c.-770T>C upstream_gene_variant 0.35 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. 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 2288730 p.Ala171Val missense_variant 0.42 pyrazinamide Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.41 ethambutol Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.41 ethambutol Assoc w R
ethA 4326250 p.Tyr408* stop_gained 0.2 ethionamide Assoc w R
gid 4408115 c.87delC frameshift_variant 0.2 streptomycin 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
Rv0010c 13905 c.-347G>T upstream_gene_variant 0.25 isoniazid
fgd1 491742 c.960T>C synonymous_variant 0.99 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.29 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.41 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.33 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.64 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.61 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764822 p.Asp485Tyr missense_variant 0.38 rifampicin Uncertain significance
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 0.97 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.31 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.37 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253952 p.Ala195Pro missense_variant 0.22 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 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 0.38 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 0.27 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
katG 2154724 p.Arg463Leu missense_variant 0.99 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.99 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.3 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
pncA 2289047 c.195C>T synonymous_variant 0.57 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.65 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.66 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.66 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087862 p.Gly348Glu missense_variant 0.28 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.37 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 0.36 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.66 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.62 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.65 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 0.33 ethambutol Not assoc w R
embA 4245131 c.1899G>A synonymous_variant 0.28 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.29 ethambutol Not assoc w R
ethA 4327415 p.Ala20Val missense_variant 0.3 ethionamide Uncertain significance
whiB6 4338194 p.Arg110Trp missense_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338242 p.Gln94* stop_gained 0.35 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 0.99 streptomycin Not assoc w R
gid 4407742 p.Arg154Pro missense_variant 0.37 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.29 streptomycin Not assoc w R