TB-Profiler result

Run: SRR3105752
Summary

Run ID: SRR3105752

Sample name:

Date: 2024-04-16T11:06:14.653334

Number of reads: 6128604

Percentage reads mapped: 98.82

Median coverage: 104.0

Strain: lineage1.2.2.2;lineage4.1.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.74
lineage1.2.2.2 Indo-Oceanic RD239 0.72
lineage4.1 Euro-American None 0.25
lineage4.1.2 Euro-American None 0.27
lineage4 Euro-American None 0.27
lineage1 Indo-Oceanic RD239 0.7
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
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA p.Thr160Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.351dupG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid ddn p.Trp139* Assoc w R - Interim
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 761095 p.Leu430Pro missense_variant 0.14 rifampicin Assoc w R
rpoB 761110 p.Asp435Gly missense_variant 0.18 rifampicin Assoc w R - Interim
rpoB 761155 p.Ser450Leu missense_variant 0.81 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.29 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288764 p.Thr160Pro missense_variant 0.3 pyrazinamide Assoc w R
eis 2715342 c.-10G>A upstream_gene_variant 0.8 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
ddn 3987259 p.Trp139* stop_gained 0.23 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 0.28 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.78 ethambutol Assoc w R
gid 4407851 c.351dupG frameshift_variant 0.69 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 5075 c.-165C>T upstream_gene_variant 0.71 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.7 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.79 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 0.72 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.73 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 0.72 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.66 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.68 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.84 isoniazid Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.18 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.77 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.34 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.84 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.68 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.28 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.65 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.8 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 764263 c.894G>A synonymous_variant 0.25 rifampicin Not assoc w R
rpoC 765148 c.1779C>T synonymous_variant 0.82 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 0.17 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 775895 c.2586C>T synonymous_variant 0.28 clofazimine
bedaquiline
mmpL5 776100 p.Thr794Ile missense_variant 0.69 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777320 c.1161C>G synonymous_variant 0.21 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800200 c.-609C>G upstream_gene_variant 0.25 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.8 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.64 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.71 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.71 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.77 ethambutol
rrs 1471644 n.-202T>C upstream_gene_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.74 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 0.71 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 0.76 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.7 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.83 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.76 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
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.78 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518076 c.-39C>T upstream_gene_variant 0.28 isoniazid
kasA 2518132 c.18C>T synonymous_variant 0.73 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.78 isoniazid
Rv2681 2997508 p.Thr257Ile missense_variant 0.6 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.78 ethionamide Uncertain significance
Rv3236c 3611974 c.1143A>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.68 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 0.68 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.71 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.78 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
embC 4240671 p.Thr270Ile missense_variant 0.71 ethambutol Not assoc w R
embC 4240975 c.1113C>T synonymous_variant 0.73 ethambutol Not assoc w R - Interim
embC 4241042 p.Asn394Asp missense_variant 0.6 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.24 ethambutol Not assoc w R
embB 4245710 c.-804G>A upstream_gene_variant 0.74 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.72 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.69 ethambutol Not assoc w R
embB 4247828 p.Ala439Thr missense_variant 0.67 ethambutol Uncertain significance
ubiA 4269307 p.Phe176Ser missense_variant 0.3 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.71 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.66 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.72 ethionamide Not assoc w R - Interim
ethA 4326197 p.Val426Gly missense_variant 0.27 ethionamide
ethA 4326439 p.Asn345Lys missense_variant 0.82 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.72 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
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 0.8 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 0.67 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.7 streptomycin Not assoc w R