TB-Profiler result

Run: SRR25827744
Summary

Run ID: SRR25827744

Sample name:

Date: 2024-04-15T23:23:11.257623

Number of reads: 9830290

Percentage reads mapped: 98.83

Median coverage: 330.0

Strain: lineage1.1.3.1;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 0.55
lineage2 East-Asian RD105 0.41
lineage1.1 Indo-Oceanic RD239 0.58
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.4
lineage2.2 East-Asian (Beijing) RD105;RD207 0.42
lineage1 Indo-Oceanic RD239 0.56
lineage1.1.3.1 Indo-Oceanic RD239 0.56
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
rpoC p.Ile491Thr Uncertain significance Mutation from literature
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
pyrazinamide pncA p.Ile5Ser 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 eis c.-12C>T Assoc w R
cycloserine
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
ethA c.1203delT Assoc w R
clofazimine
para-aminosalicylic_acid thyA p.Thr22Ala Mutation from literature
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 0.36 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.48 rifampicin Assoc w R
rpoC 764841 p.Ile491Thr missense_variant 0.35 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.4 streptomycin Assoc w R
inhA 1673423 c.-779G>T upstream_gene_variant 0.4 isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
katG 2155168 p.Ser315Thr missense_variant 0.4 isoniazid Assoc w R High-level resistance
pncA 2289228 p.Ile5Ser missense_variant 0.42 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.39 kanamycin Assoc w R
thyA 3074408 p.Thr22Ala missense_variant 0.42 para-aminosalicylic_acid Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.42 ethambutol Uncertain significance Mutation from literature
ethA 4326270 c.1203delT frameshift_variant 0.38 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
gyrB 6112 p.Met291Ile missense_variant 0.59 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 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.53 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 0.57 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.53 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.98 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.42 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.43 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.4 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.4 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.58 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.55 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.97 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.54 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.54 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.63 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.6 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 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.42 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779526 c.-621G>A upstream_gene_variant 0.59 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 0.44 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 0.62 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.99 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.43 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.48 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.49 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.56 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.42 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.55 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.55 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
tlyA 1918254 c.315C>T synonymous_variant 0.59 capreomycin
bacA 2062922 p.Ile603Val missense_variant 0.54 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2102380 c.663G>T synonymous_variant 0.54 ethionamide
delamanid
isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.98 isoniazid Not assoc w R
katG 2155416 c.696G>A synonymous_variant 0.54 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.56 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.57 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
kasA 2518132 c.18C>T synonymous_variant 0.56 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.57 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.54 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 3067949 c.-4C>T upstream_gene_variant 0.48 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.56 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.4 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.56 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 0.43 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841253 c.168C>T synonymous_variant 0.45 cycloserine
rpoA 3878637 c.-130G>C upstream_gene_variant 0.22 rifampicin
clpC1 4040517 p.Val63Ala missense_variant 0.54 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.56 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 0.57 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.43 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.58 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 0.43 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.53 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.58 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.54 ethambutol Not assoc w R
embB 4247847 p.Gln445Arg missense_variant 0.32 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.33 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.61 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.55 ethambutol Not assoc w R
ethA 4327546 c.-73T>A upstream_gene_variant 0.51 ethionamide
whiB6 4338292 p.Ala77Val missense_variant 0.43 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.99 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.4 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.54 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.57 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.38 streptomycin Not assoc w R