TB-Profiler result

Run: SRR17657949
Summary

Run ID: SRR17657949

Sample name:

Date: 2024-04-16T09:05:43.289663

Number of reads: 2399766

Percentage reads mapped: 99.6

Median coverage: 50.0

Strain: lineage1.1.2;lineage4.3.4.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.4
lineage4.3 Euro-American (LAM) None 0.58
lineage1.1 Indo-Oceanic RD239 0.47
lineage4 Euro-American None 0.6
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.59
lineage1 Indo-Oceanic RD239 0.43
lineage4.3.4 Euro-American (LAM) RD174 0.59
lineage4.3.4.2 Euro-American (LAM) RD174 0.54
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
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
ahpC 2726145 c.-48G>A upstream_gene_variant 0.51 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.53 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.53 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 6112 p.Met291Ile missense_variant 0.51 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.5 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6140 p.Val301Leu missense_variant 0.42 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 0.57 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.35 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 0.55 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.45 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.54 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.52 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.38 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.36 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.48 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.46 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.64 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.56 rifampicin Not assoc w R
rpoC 765312 p.Ala648Asp missense_variant 0.49 rifampicin Uncertain significance
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 0.51 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 778696 c.206_209dupTCAA frameshift_variant 0.51 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.32 linezolid Not assoc w R
Rv1129c 1254159 p.Arg126Trp missense_variant 0.47 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.48 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1304743 p.Ile605Val missense_variant 0.46 clofazimine
pretomanid
delamanid
embR 1417019 p.Cys110Tyr missense_variant 0.28 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.3 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.45 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.36 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.28 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 0.42 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 0.32 isoniazid Not assoc w R
katG 2154953 p.Asp387His missense_variant 0.53 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.46 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.56 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.61 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2222641 p.Ser175Leu missense_variant 0.64 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289781 c.-540C>A upstream_gene_variant 0.43 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.57 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.41 isoniazid
folC 2746258 c.1341C>T synonymous_variant 0.32 para-aminosalicylic_acid
folC 2746488 p.Asp371Tyr missense_variant 0.33 para-aminosalicylic_acid
pepQ 2860017 c.402T>C synonymous_variant 0.7 clofazimine
bedaquiline Not assoc w R - Interim
Rv2681 2996912 c.174C>T synonymous_variant 0.35 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.38 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
thyA 3073868 p.Thr202Ala missense_variant 0.54 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.41 ethionamide Uncertain significance
Rv3083 3448721 p.Lys73Thr missense_variant 0.38 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.64 pyrazinamide Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.32 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.59 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.62 pyrazinamide Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.5 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.47 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 4139739 p.Leu6Pro missense_variant 0.38 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240671 p.Thr270Ile missense_variant 0.38 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.33 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243245 p.Gly5Arg missense_variant 0.36 ethambutol Uncertain significance
embA 4243848 p.Val206Met missense_variant 0.33 ethambutol Not assoc w R
embA 4244148 p.Trp306Arg missense_variant 0.54 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.4 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.47 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.54 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.38 ethambutol Not assoc w R
ethA 4326113 p.Pro454Leu missense_variant 0.49 ethionamide Uncertain significance
ethA 4326953 p.Asp174Gly missense_variant 0.55 ethionamide Uncertain significance
whiB6 4338289 p.Gly78Glu missense_variant 0.45 capreomycin Uncertain significance
amikacin
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 0.57 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 0.41 streptomycin Not assoc w R
gid 4408125 p.Leu26Phe missense_variant 0.55 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.5 streptomycin Not assoc w R