TB-Profiler result

Run: SRR11662691

Summary

Run ID: SRR11662691

Sample name:

Date: 2024-04-14T12:52:56.056237

Number of reads: 12791442

Percentage reads mapped: 99.06

Median coverage: 369.0

Strain: lineage1.1.3.3;lineage2.2.1

Spoligotype:

Drug-resistance: Pre-XDR-TB


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.3 Indo-Oceanic RD239 0.78
lineage2 East-Asian RD105 0.23
lineage1.1.3.3 Indo-Oceanic RD239 0.78
lineage1.1 Indo-Oceanic RD239 0.79
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.22
lineage2.2 East-Asian (Beijing) RD105;RD207 0.23
lineage1 Indo-Oceanic RD239 0.78
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Arg Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA c.441dupA Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.639_640delGT Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.26 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761140 p.His445Arg missense_variant 0.21 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.24 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.23 isoniazid Assoc w R High-level resistance
pncA 2288800 c.441dupA frameshift_variant 0.23 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.2 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.18 ethambutol Uncertain significance Mutation from literature
ethA 4326833 c.639_640delGT frameshift_variant 0.19 ethionamide 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
dnaA 817 p.Ile273Val missense_variant 0.75 isoniazid Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.72 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 8297 c.996C>T synonymous_variant 0.8 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8452 p.Ala384Val missense_variant 0.82 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.76 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 0.79 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.79 isoniazid Not assoc w R
Rv0010c 13636 c.-78A>G upstream_gene_variant 0.24 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.23 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.23 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.22 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.21 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.8 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.79 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 0.77 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.78 rifampicin Not assoc w R
rpoC 765050 p.Ser561Pro missense_variant 0.18 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.78 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.75 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 776182 p.Asp767Asn missense_variant 0.2 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.24 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.75 linezolid Not assoc w R
Rv1129c 1254144 p.Thr131Pro missense_variant 0.19 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
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
fbiC 1303312 p.Ile128Val missense_variant 0.22 clofazimine
pretomanid
delamanid
Rv1258c 1406760 c.580_581insC frameshift_variant 0.2 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.74 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.76 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.78 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475049 n.1392C>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.74 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.76 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 0.8 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
katG 2156146 c.-35A>G upstream_gene_variant 0.79 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.8 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.78 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2222369 p.Ile266Val missense_variant 0.77 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223712 c.-548G>A upstream_gene_variant 0.76 clofazimine
bedaquiline
kasA 2518132 c.18C>T synonymous_variant 0.77 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.74 isoniazid
folC 2746365 c.1234C>T synonymous_variant 0.78 para-aminosalicylic_acid
Rv2681 2997944 c.1206C>T synonymous_variant 0.8 capreomycin Not assoc w R - Interim
Rv2752c 3064632 c.1560C>T synonymous_variant 0.74 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
thyX 3067963 c.-18G>T upstream_gene_variant 0.23 para-aminosalicylic_acid
thyA 3073819 c.652delC frameshift_variant 0.22 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.77 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.18 pyrazinamide Not assoc w R - Interim
Rv3236c 3613023 p.Pro32Ala missense_variant 0.2 pyrazinamide
lpqB 3623435 c.1476G>A synonymous_variant 0.83 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.81 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 3626562 p.Pro18Ser missense_variant 0.18 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642709 p.Gly392Ala missense_variant 0.81 clofazimine
pretomanid
delamanid
clpC1 4040517 p.Val63Ala missense_variant 0.78 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.79 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 4138749 p.Gln336Arg missense_variant 0.42 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139183 c.572dupG frameshift_variant 0.2 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139698 p.Ile20Val missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240671 p.Thr270Ile missense_variant 0.84 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.79 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.23 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.83 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.78 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.76 ethambutol Not assoc w R
aftB 4266975 p.Pro621Arg missense_variant 0.79 ethambutol Uncertain significance
aftB 4267431 p.Ser469Leu missense_variant 0.79 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.2 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.76 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.79 ethambutol Not assoc w R
ethA 4328299 c.-826A>T upstream_gene_variant 0.16 ethionamide
whiB6 4338365 p.Cys53Gly missense_variant 0.2 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 0.8 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 1.0 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.81 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.79 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.2 streptomycin Not assoc w R