TB-Profiler result

Run: SRR19573671
Summary

Run ID: SRR19573671

Sample name:

Date: 2024-10-04T02:30:52.594164

Number of reads: 15116906

Percentage reads mapped: 98.05

Median coverage: 175.5

Strain: lineage1.2.2.2

Spoligotype:

Drug-resistance: Other

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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 0.99
lineage1.2.2.2 Indo-Oceanic RD239 1.0
lineage1 Indo-Oceanic RD239 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide
streptomycin
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
embB 4248003 p.Gln497Arg missense_variant 0.33 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 5075 c.-165C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 5078 c.-162_-161insG upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 1.0 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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 1.0 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 1.0 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.99 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13548 p.Thr4Ile missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.82 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
mshA 575092 c.-256C>A upstream_gene_variant 0.17 isoniazid
ethionamide
mshA 575121 c.-227G>C upstream_gene_variant 0.2 isoniazid
ethionamide
mshA 575265 c.-83C>A upstream_gene_variant 0.27 isoniazid
ethionamide
mshA 576337 c.990G>A synonymous_variant 0.27 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
Rv0565c 656322 c.1149C>T synonymous_variant 0.5 ethionamide
Rv0565c 656991 c.480G>A synonymous_variant 0.24 ethionamide
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 1.0 rifampicin Not assoc w R
mmaA3 737374 p.Ile259Ser missense_variant 0.18 isoniazid
mmaA3 737609 p.Lys181Glu missense_variant 0.33 isoniazid
rpoB 759670 c.-137C>T upstream_gene_variant 0.15 rifampicin Uncertain significance
rpoB 761012 p.Asp402Glu missense_variant 0.22 rifampicin
rpoB 761748 p.Ser648Thr missense_variant 0.32 rifampicin
rpoB 761786 c.1980C>T synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 761863 p.Ala686Val missense_variant 0.99 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763321 p.Ala1172Val missense_variant 0.69 rifampicin
rpoC 763884 p.Ala172Val missense_variant 1.0 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764002 c.633C>T synonymous_variant 0.96 rifampicin
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
mmpL5 778483 c.-3C>T upstream_gene_variant 0.12 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Not assoc w R
rplC 800815 p.Arg3* stop_gained 0.27 linezolid
rplC 800838 p.Lys10Asn missense_variant 0.17 linezolid
Rv1129c 1253587 c.948C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254747 c.-213C>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
fbiC 1304750 p.Pro607Leu missense_variant 0.72 pretomanid
delamanid
clofazimine
embR 1417019 p.Cys110Tyr missense_variant 0.73 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.89 ethambutol
embR 1417933 c.-587_-586insT upstream_gene_variant 0.26 ethambutol
embR 1417933 c.-586G>T upstream_gene_variant 0.64 ethambutol
atpE 1460975 c.-70G>A upstream_gene_variant 0.2 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.11 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474625 n.968T>G non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1474711 n.1054_1055insC non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475601 n.1944C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
tsnR 1853763 p.Ala53Val missense_variant 0.57 linezolid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 1.0 linezolid Not assoc w R
tsnR 1854038 p.Asp145Asn missense_variant 0.44 linezolid
tsnR 1854144 p.Ala180Val missense_variant 0.29 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 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2102078 p.Asp322Val missense_variant 0.22 isoniazid
delamanid
ethionamide
ndh 2102242 c.801G>A synonymous_variant 0.71 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155668 c.444G>A synonymous_variant 0.57 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2222519 p.Gly216Ser missense_variant 0.85 bedaquiline
clofazimine
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 1.0 bedaquiline Uncertain significance
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
eis 2715261 c.72C>T synonymous_variant 0.23 kanamycin
amikacin
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
ahpC 2726693 c.501C>T synonymous_variant 0.36 isoniazid
folC 2746509 p.Gln364* stop_gained 0.45 para-aminosalicylic_acid
folC 2747542 c.57C>T synonymous_variant 0.89 para-aminosalicylic_acid
Rv2477c 2783487 p.Pro186Ala missense_variant 0.21 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
pepQ 2859323 p.Pro366Ser missense_variant 0.25 bedaquiline
clofazimine
Rv2681 2997883 p.Cys382Tyr missense_variant 0.75 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3086953 p.Ile45Thr missense_variant 0.35 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.96 ethionamide Uncertain significance
whiB7 3568821 c.-142A>C upstream_gene_variant 0.2 kanamycin
amikacin
streptomycin
lpqB 3623551 p.Arg454Cys missense_variant 0.36 rifampicin
bedaquiline
lpqB 3624486 p.Asp142Gly missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3625492 c.-582C>T upstream_gene_variant 0.2 rifampicin
bedaquiline
lpqB 3625587 c.-677C>T upstream_gene_variant 0.46 rifampicin
bedaquiline
mtrB 3626467 c.147G>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
rpoA 3878817 c.-310T>A upstream_gene_variant 1.0 rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 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 4240276 c.414G>A synonymous_variant 0.78 ethambutol
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Not assoc w R
embA 4246312 p.Gly1027Ala missense_variant 0.21 ethambutol
embA 4246314 p.Gly1028Arg missense_variant 0.38 ethambutol
embA 4246359 p.Ala1043Thr missense_variant 0.21 ethambutol
embB 4247512 c.999T>C synonymous_variant 0.24 ethambutol
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4247889 p.Gly459Asp missense_variant 0.28 ethambutol
aftB 4267055 c.1782C>T synonymous_variant 0.62 ethambutol
aftB 4267472 c.1365C>G synonymous_variant 0.19 ethambutol
aftB 4268560 p.Leu93Met missense_variant 0.48 ethambutol
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326019 c.1455C>T synonymous_variant 0.32 ethionamide Not assoc w R - Interim
ethA 4326148 c.1326G>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 1.0 ethionamide Uncertain significance
ethR 4327828 p.Pro94Ser missense_variant 0.79 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 1.0 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 4407873 c.330G>T synonymous_variant 0.96 streptomycin Not assoc w R
gid 4408013 p.Arg64Trp missense_variant 0.93 streptomycin Uncertain significance