TB-Profiler result

Run: SRR2100207
Summary

Run ID: SRR2100207

Sample name:

Date: 2024-10-04T09:49:23.728716

Number of reads: 5735119

Percentage reads mapped: 99.35

Median coverage: 127.0

Strain: lineage1.2.2.2;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 0.29
lineage1.2.2 Indo-Oceanic RD239 0.73
lineage1.2.2.2 Indo-Oceanic RD239 0.72
lineage1 Indo-Oceanic RD239 0.72
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 rpsL p.Lys43Arg 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
rpsL 781687 p.Lys43Arg missense_variant 0.27 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.3 isoniazid Assoc w R High-level resistance
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 5075 c.-165C>T upstream_gene_variant 0.69 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.65 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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.69 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8668 p.Ala456Val missense_variant 0.65 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9143 c.1842T>C synonymous_variant 0.69 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9801 p.Asp834Asn missense_variant 0.72 levofloxacin Uncertain significance
moxifloxacin
Rv0010c 13298 p.Ile87Met missense_variant 0.73 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.63 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.62 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.77 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.26 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.75 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.66 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.32 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.3 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 0.76 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.76 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 1.0 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
rplC 800357 c.-452C>A upstream_gene_variant 0.69 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.79 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.65 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.76 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.61 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 0.69 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin 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 2168742 p.Gly624Asp missense_variant 0.72 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.68 bedaquiline Not assoc w R - Interim
clofazimine 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
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.64 bedaquiline Uncertain significance
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.23 pyrazinamide Not assoc w R
pncA 2289348 c.-107T>G upstream_gene_variant 0.29 pyrazinamide
pncA 2289365 c.-125delC upstream_gene_variant 0.31 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.78 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.72 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.3 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.31 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
fbiD 3339592 p.His159Asn missense_variant 0.8 pretomanid
delamanid
clofazimine
Rv3083 3448714 p.Asp71His missense_variant 0.68 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.67 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624557 c.354T>C synonymous_variant 0.65 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.72 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
alr 3841473 c.-53G>A upstream_gene_variant 0.32 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.75 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.3 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.68 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.29 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 4240671 p.Thr270Ile missense_variant 0.78 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.76 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.33 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.72 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.73 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.73 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.67 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.72 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.7 ethionamide Uncertain significance
ethR 4327672 c.124C>T synonymous_variant 0.25 ethionamide Not assoc w R - Interim
whiB6 4338203 p.Arg107Cys missense_variant 0.76 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin 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 4338603 c.-82C>T upstream_gene_variant 0.7 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 1.0 streptomycin Not assoc w R
gid 4407742 p.Arg154Pro missense_variant 0.69 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.68 streptomycin Not assoc w R