TB-Profiler result

Run: SRR25827574
Summary

Run ID: SRR25827574

Sample name:

Date: 2024-04-15T20:42:07.386464

Number of reads: 3843146

Percentage reads mapped: 49.71

Median coverage: 107.0

Strain: lineage1.1.3.2;lineage3.1.2

Spoligotype:

Drug-resistance: MDR-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 0.47
lineage1.1.3 Indo-Oceanic RD239 0.43
lineage1.1.3.2 Indo-Oceanic RD239 0.45
lineage3.1.2 East-African-Indian RD750 0.47
lineage1.1 Indo-Oceanic RD239 0.47
lineage1 Indo-Oceanic RD239 0.51
lineage3.1 East-African-Indian RD750 0.52
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
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
rpoB 761155 p.Ser450Leu missense_variant 0.6 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.59 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.5 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.53 ethambutol 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
gyrB 6112 p.Met291Ile missense_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8188 p.Leu296Pro missense_variant 0.37 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8452 p.Ala384Val missense_variant 0.56 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.44 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 13298 p.Ile87Met missense_variant 0.44 isoniazid Not assoc w R
Rv0010c 13564 c.-6G>A upstream_gene_variant 0.5 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 574579 c.-769T>C upstream_gene_variant 0.5 ethionamide
isoniazid
ccsA 619695 c.-196G>A upstream_gene_variant 0.35 capreomycin
amikacin
kanamycin
Rv0565c 657081 c.390G>A synonymous_variant 0.48 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.55 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.55 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.45 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.39 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.47 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.47 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.36 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.51 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.46 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpR5 779033 p.Asp15Gly missense_variant 0.5 clofazimine Uncertain significance
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.5 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254743 c.-209C>T upstream_gene_variant 0.49 moxifloxacin
levofloxacin
rifampicin
isoniazid
sigE 1364199 c.-214G>A upstream_gene_variant 0.41 pyrazinamide
embR 1417019 p.Cys110Tyr missense_variant 0.5 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.55 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.47 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.46 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.46 linezolid Not assoc w R
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 2062922 p.Ile603Val missense_variant 0.44 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2064420 c.309C>T synonymous_variant 0.47 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2102200 c.843G>A synonymous_variant 0.49 ethionamide
delamanid
isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.36 pyrazinamide Uncertain significance
PPE35 2168604 p.Pro670Leu missense_variant 0.53 pyrazinamide Not assoc w R
PPE35 2168719 p.Thr632Pro missense_variant 0.55 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.48 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.42 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.48 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.45 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.51 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.5 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.43 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.57 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
thyX 3068145 c.-200C>T upstream_gene_variant 0.52 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.47 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.52 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642173 c.639G>A synonymous_variant 0.41 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rpoA 3878687 c.-180A>C upstream_gene_variant 0.61 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.43 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.5 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.49 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.44 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.45 ethambutol Not assoc w R
embC 4240774 c.912C>A synonymous_variant 0.44 ethambutol
embC 4240807 c.945C>T synonymous_variant 0.49 ethambutol Not assoc w R - Interim
embC 4241042 p.Asn394Asp missense_variant 0.5 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.39 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.49 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.39 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.42 ethambutol Not assoc w R
embB 4248781 c.2268G>A synonymous_variant 0.56 ethambutol Not assoc w R - Interim
embB 4248940 c.2427C>T synonymous_variant 0.41 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 0.53 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.44 ethambutol Not assoc w R
ethA 4326686 c.737_787delAGGCGGCCGTGTACAGCGCCTGCCAGAAGTGGCCACGGCGCATGCGGAAGA disruptive_inframe_deletion 0.33 ethionamide
ethA 4327124 p.Thr117Ile missense_variant 0.45 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.46 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407547 p.Ala219Val missense_variant 0.51 streptomycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.54 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.51 streptomycin Not assoc w R