TB-Profiler result

Run: SRR5341451
Summary

Run ID: SRR5341451

Sample name:

Date: 2024-03-26T23:53:55.020629

Number of reads: 5472221

Percentage reads mapped: 98.16

Median coverage: 145.0

Strain: lineage1.1.2;lineage3

Spoligotype:

Drug-resistance: HR-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 0.18
lineage1.1.2 Indo-Oceanic RD239 0.84
lineage1.1 Indo-Oceanic RD239 0.84
lineage1 Indo-Oceanic RD239 0.82
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rrs n.517C>T Assoc w R
gid c.351delG 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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.26 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid Assoc w R High-level resistance
gid 4407851 c.351delG frameshift_variant 0.77 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
gyrB 6112 p.Met291Ile missense_variant 0.78 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.77 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 8452 p.Ala384Val missense_variant 0.83 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.72 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 0.85 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.88 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.18 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.81 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.81 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.82 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.18 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.82 rifampicin Not assoc w R
rpoC 762371 c.-999G>A upstream_gene_variant 0.78 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 0.19 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 0.9 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.9 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.83 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
mmpL5 776395 p.Phe696Leu missense_variant 0.81 clofazimine Not assoc w R
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800211 c.-598G>A upstream_gene_variant 0.84 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.84 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
embR 1416631 c.717C>A synonymous_variant 0.23 ethambutol Not assoc w R - Interim
embR 1417019 p.Cys110Tyr missense_variant 0.8 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.8 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.81 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.84 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.8 linezolid Not assoc w R
tsnR 1854089 p.Ile162Val missense_variant 0.21 linezolid
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 0.81 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
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 0.86 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.83 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 0.16 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.18 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.79 isoniazid
eis 2715016 p.Arg106His missense_variant 0.83 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.86 isoniazid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.17 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
pepQ 2860398 c.21A>C synonymous_variant 0.84 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
Rv2680 2995892 c.-212delA upstream_gene_variant 0.9 capreomycin
Rv2681 2996912 c.174C>T synonymous_variant 0.82 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.88 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3086987 p.Gln56His missense_variant 0.79 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.85 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.88 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.83 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
alr 3841473 c.-53G>A upstream_gene_variant 0.15 cycloserine
clpC1 4038338 c.2364_2366dupGAT disruptive_inframe_insertion 0.76 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.9 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.87 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.12 pyrazinamide
panD 4045262 c.-981G>A upstream_gene_variant 0.88 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.77 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 0.18 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 0.85 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.86 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 0.77 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.82 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.84 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.81 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.83 ethambutol Not assoc w R
ethA 4326983 p.Pro164Leu missense_variant 0.16 ethionamide Uncertain significance
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 0.81 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 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.76 streptomycin Not assoc w R