TB-Profiler result

Run: SRR28351324
Summary

Run ID: SRR28351324

Sample name:

Date: 2024-10-05T12:11:12.163913

Number of reads: 7730854

Percentage reads mapped: 99.7

Median coverage: 226.5

Strain: lineage3;lineage4.4.1.2

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 0.29
lineage4.4.1.2 Euro-American None 0.67
lineage4.4.1 Euro-American (S-type) None 0.69
lineage4 Euro-American None 0.7
lineage4.4 Euro-American None 0.68
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.Asp435Gly Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Ser450Leu Assoc w R
rpoC p.Leu527Val Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
p.Glu504Asp Uncertain significance Mutation from literature
pyrazinamide
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Tyr Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Tyr Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
gyrA 7581 p.Asp94Tyr missense_variant 0.81 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761095 p.Leu430Pro missense_variant 0.71 rifampicin Assoc w R
rpoB 761110 p.Asp435Gly missense_variant 0.72 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761155 p.Ser450Leu missense_variant 0.23 rifampicin Assoc w R
rpoC 764948 p.Leu527Val missense_variant 0.27 rifampicin Uncertain significance Mutation from literature
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.19 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.26 ethambutol Assoc w R
embB 4248025 p.Glu504Asp missense_variant 0.6 ethambutol Uncertain significance Mutation from literature
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 0.15 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.21 ethionamide Not assoc w R - Interim
mmaA3 737899 p.Val84Gly missense_variant 0.24 isoniazid
rpoB 759746 c.-61C>T upstream_gene_variant 0.22 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.4 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.25 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 0.28 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.41 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406221 p.Ala374Pro missense_variant 0.3 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833804 p.Ala88Gly missense_variant 0.39 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917670 c.-270G>A upstream_gene_variant 0.36 capreomycin
tlyA 1917851 c.-89C>A upstream_gene_variant 0.24 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 0.68 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.34 isoniazid Not assoc w R
PPE35 2167770 p.Ser948Ile missense_variant 0.76 pyrazinamide Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.21 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.77 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 0.3 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.37 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.25 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.36 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
Rv2477c 2783786 p.Arg86His missense_variant 0.26 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Not assoc w R
amikacin Uncertain significance
pepQ 2860213 p.Pro69Leu missense_variant 0.61 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2681 2997175 p.Arg146Gln missense_variant 0.71 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.68 ethionamide Not assoc w R - Interim
Rv3236c 3613591 c.-475G>A upstream_gene_variant 0.25 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.28 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.35 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 4238963 c.-900C>T upstream_gene_variant 0.67 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.32 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243218 c.-15C>G upstream_gene_variant 0.64 ethambutol Uncertain significance
embB 4249012 c.2499G>A synonymous_variant 0.66 ethambutol Not assoc w R
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 0.99 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.22 streptomycin Not assoc w R
gid 4407946 p.Leu86His missense_variant 0.7 streptomycin Uncertain significance