TB-Profiler result

Run: SRR2100270
Summary

Run ID: SRR2100270

Sample name:

Date: 2024-10-05T13:07:38.894483

Number of reads: 14480339

Percentage reads mapped: 99.4

Median coverage: 290.0

Strain: lineage1.2.2.2;lineage4.1.1.3

Spoligotype:

Drug-resistance: HR-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 0.26
lineage1.2.2.2 Indo-Oceanic RD239 0.25
lineage4.1 Euro-American None 0.73
lineage4.1.1.3 Euro-American (X-type) RD193 0.74
lineage4 Euro-American None 0.73
lineage4.1.1 Euro-American (X-type) None 0.74
lineage1 Indo-Oceanic RD239 0.25
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 gid c.102delG 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
katG 2155168 p.Ser315Thr missense_variant 0.78 isoniazid Assoc w R High-level resistance
gid 4408100 c.102delG frameshift_variant 0.27 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 0.28 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.19 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.29 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 7532 c.231T>C synonymous_variant 0.3 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.3 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.25 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
gyrA 9782 c.2481C>A synonymous_variant 0.24 levofloxacin
moxifloxacin
Rv0010c 13298 p.Ile87Met missense_variant 0.21 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.29 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.27 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.24 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.25 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 656180 p.Asp431Asn missense_variant 0.3 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.7 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.31 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.18 rifampicin Not assoc w R
rpoB 760865 c.1059C>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.28 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.29 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.78 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 0.24 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 800219 c.-590T>C upstream_gene_variant 0.72 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.31 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.26 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 0.26 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.28 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.2 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833684 p.Arg48Pro missense_variant 0.76 pyrazinamide
rpsA 1834130 p.Glu197Lys missense_variant 0.77 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.33 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 0.27 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 0.23 isoniazid Not assoc w R
PPE35 2167683 p.Leu977Arg missense_variant 0.28 pyrazinamide Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.23 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.2 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.25 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 0.23 bedaquiline Uncertain significance
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.31 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.14 isoniazid
Rv2681 2997949 p.Arg404His missense_variant 0.33 capreomycin
thyX 3067901 c.45C>T synonymous_variant 0.73 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.34 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.26 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.28 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
rpoA 3878817 c.-310T>A upstream_gene_variant 0.24 rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.25 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.23 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
embC 4240671 p.Thr270Ile missense_variant 0.23 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.32 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 0.78 ethambutol Not assoc w R
embA 4243622 c.390G>A synonymous_variant 0.78 ethambutol Not assoc w R - Interim
embA 4244456 c.1224C>G synonymous_variant 0.26 ethambutol Not assoc w R - Interim
embA 4245969 p.Pro913Ser missense_variant 0.23 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.25 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.71 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.23 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.36 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.24 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.25 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.29 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 0.26 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 0.26 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.23 streptomycin Not assoc w R