TB-Profiler result

Run: ERR12328154
Summary

Run ID: ERR12328154

Sample name:

Date: 2024-04-15T20:33:52.133478

Number of reads: 2525915

Percentage reads mapped: 99.58

Median coverage: 75.0

Strain: lineage1.1.1.1;lineage2.2.1;lineage4.2.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.17
lineage2 East-Asian RD105 0.74
lineage4.2 Euro-American None 0.16
lineage1.1 Indo-Oceanic RD239 0.11
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.71
lineage2.2 East-Asian (Beijing) RD105;RD207 0.66
lineage4 Euro-American None 0.19
lineage1 Indo-Oceanic RD239 0.12
lineage1.1.1 Indo-Oceanic RD239 0.13
lineage1.1.1.1 Indo-Oceanic RD239 0.1
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin rrs n.517C>T 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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.79 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 6112 p.Met291Ile missense_variant 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 6961 c.-341G>A upstream_gene_variant 0.79 levofloxacin
moxifloxacin
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 9026 c.1725G>A synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 9143 c.1842T>C synonymous_variant 0.15 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
fgd1 491742 c.960T>C synonymous_variant 0.73 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.71 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576077 c.730C>T synonymous_variant 0.2 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.77 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657014 p.Thr153Ala missense_variant 0.74 ethionamide
Rv0565c 657081 c.390G>A synonymous_variant 0.77 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.7 ethionamide Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.16 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.79 rifampicin Not assoc w R
rpoC 765157 c.1788C>T synonymous_variant 0.12 rifampicin
rpoC 765171 p.Pro601Leu missense_variant 0.11 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 0.88 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.68 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 777394 c.1087C>A synonymous_variant 0.15 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 0.62 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.15 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.19 linezolid Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.12 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.8 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1304962 p.Trp678Gly missense_variant 0.12 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.7 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.21 ethambutol
embR 1418041 c.-694T>C upstream_gene_variant 0.73 ethambutol
rrs 1471647 n.-199G>C upstream_gene_variant 0.75 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.67 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.16 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.18 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 0.15 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.82 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.89 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.21 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.11 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
pncA 2289463 c.-222C>G upstream_gene_variant 0.16 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.18 isoniazid
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.12 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.14 ethionamide Uncertain significance
Rv3236c 3612469 c.648A>G synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
Rv3236c 3612813 p.Thr102Ala missense_variant 0.7 pyrazinamide Not assoc w R - Interim
Rv3236c 3613837 c.-721G>A upstream_gene_variant 0.19 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.7 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841472 c.-52C>T upstream_gene_variant 0.13 cycloserine
glpK 4138377 p.Val460Ala missense_variant 0.1 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 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.67 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.17 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.13 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.17 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.53 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.15 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.14 ethambutol Not assoc w R
ethA 4328331 c.-858C>T upstream_gene_variant 0.14 ethionamide
whiB6 4338296 p.Trp76Arg missense_variant 0.76 capreomycin
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 0.84 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.78 streptomycin Not assoc w R