TB-Profiler result

Run: SRR1167183
Summary

Run ID: SRR1167183

Sample name:

Date: 2024-10-04T20:46:34.306080

Number of reads: 4582317

Percentage reads mapped: 99.53

Median coverage: 109.0

Strain: lineage3.1.1;lineage4.3.3

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
lineage3 East-African-Indian RD750 0.52
lineage4.3 Euro-American (LAM) None 0.47
lineage3.1.1 East-African-Indian RD750 0.54
lineage4 Euro-American None 0.48
lineage4.3.3 Euro-American (LAM) RD115 0.49
lineage3.1 East-African-Indian RD750 0.58
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Gly Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Leu452Pro Assoc w R
isoniazid inhA c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A. 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.Met306Val Assoc w R
pyrazinamide pncA c.456dupC Assoc w R
p.Trp68Cys Assoc w R
streptomycin gid c.107delT 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)
ofloxacin
levofloxacin gyrA p.Ala90Val 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
cycloserine
ethionamide inhA c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A
ethA c.-11A>G Uncertain significance Mutation from literature
clofazimine
para-aminosalicylic_acid
delamanid fgd1 c.230_231dupCC Assoc w R - Interim Confers DLM-PMD cross-resistance
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 7570 p.Ala90Val missense_variant 0.52 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)
fgd1 491008 c.230_231dupCC frameshift_variant 0.14 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
rpoB 761110 p.Asp435Gly missense_variant 0.47 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761161 p.Leu452Pro missense_variant 0.47 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.45 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673432 c.-770T>A upstream_gene_variant 0.47 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>A
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>A. 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 2288785 c.456dupC frameshift_variant 0.53 pyrazinamide Assoc w R
pncA 2289038 p.Trp68Cys missense_variant 0.53 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.44 ethambutol Assoc w R
ethA 4327484 c.-11A>G upstream_gene_variant 0.45 ethionamide Uncertain significance Mutation from literature
gid 4408095 c.107delT frameshift_variant 0.65 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 0.98 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 8040 p.Gly247Ser missense_variant 0.5 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 13484 c.75T>C synonymous_variant 0.52 isoniazid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.54 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.51 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.48 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.54 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.57 rifampicin Not assoc w R
rpoB 763123 p.Ile1106Thr missense_variant 0.53 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.53 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 0.45 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776222 c.2258dupG frameshift_variant 0.15 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 778086 c.393_394dupGG frameshift_variant 0.17 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.45 capreomycin Not assoc w R
linezolid Uncertain significance
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 0.54 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.52 pyrazinamide Not assoc w R
PPE35 2170461 p.Gly51Glu missense_variant 0.44 pyrazinamide Not assoc w R
Rv1979c 2223051 p.Glu38Asp missense_variant 0.41 bedaquiline Uncertain significance
clofazimine Uncertain significance
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 0.58 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.52 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.47 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.45 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.48 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
Rv2752c 3065824 p.Pro123Leu missense_variant 0.52 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.41 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.41 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.6 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.5 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 4240172 p.Val104Met missense_variant 0.58 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.59 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.51 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269271 p.Val188Ala missense_variant 0.51 ethambutol 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 0.54 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.52 streptomycin Not assoc w R