TB-Profiler result

Run: ERR9786771
Summary

Run ID: ERR9786771

Sample name:

Date: 2024-04-15T12:05:50.160722

Number of reads: 2342937

Percentage reads mapped: 99.66

Median coverage: 108.0

Strain: lineage4.3.4.1;lineage6.1.1

Spoligotype:

Drug-resistance: RR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.71
lineage6.1.1 West-Africa 2 RD702 0.33
lineage4.3.4.1 Euro-American (LAM) RD174 0.7
lineage4 Euro-American None 0.73
lineage4.3.4 Euro-American (LAM) RD174 0.7
lineage6 West-Africa 2 RD702 0.31
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu449Gln Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid
ethambutol
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
rpoB 761152 p.Leu449Gln missense_variant 0.12 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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 6446 p.Ala403Ser missense_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
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 8493 p.Leu398Phe missense_variant 0.28 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8715 p.Pro472Ser missense_variant 0.71 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9143 c.1842T>C synonymous_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.28 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.31 isoniazid Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.29 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.31 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 656432 p.Gly347Ser missense_variant 0.33 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.25 ethionamide
rpoB 759608 c.-199C>T upstream_gene_variant 0.78 rifampicin Uncertain significance
rpoB 760855 p.Thr350Ile missense_variant 0.26 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.22 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.35 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.29 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.73 rifampicin Not assoc w R
rpoC 766231 c.2862T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
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 0.35 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800232 c.-577G>T upstream_gene_variant 0.31 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.33 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.31 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
sigE 1364434 p.Arg8Trp missense_variant 0.68 pyrazinamide Not assoc w R
Rv1258c 1406685 p.Val219Ala missense_variant 0.27 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1416633 p.Leu239Val missense_variant 0.22 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.32 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.34 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674434 p.Val78Ala missense_variant 0.33 ethionamide Uncertain significance
isoniazid Not assoc w R
tsnR 1854026 p.Gly141Arg missense_variant 0.24 linezolid Uncertain significance
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 0.22 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063121 c.1608A>T synonymous_variant 0.23 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.29 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.29 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.26 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.29 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 2289706 c.-465C>A upstream_gene_variant 0.36 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.19 isoniazid
ahpC 2726323 p.Pro44Arg missense_variant 0.73 isoniazid Uncertain significance
pepQ 2859830 p.Gly197Arg missense_variant 0.65 clofazimine Uncertain significance
bedaquiline Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.73 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 0.29 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.23 cycloserine
ald 3087518 c.699C>T synonymous_variant 0.59 cycloserine
Rv3083 3448598 p.Ile32Thr missense_variant 0.65 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.68 pyrazinamide Not assoc w R
Rv3236c 3612143 p.Arg325His missense_variant 0.23 pyrazinamide Uncertain significance
Rv3236c 3612768 p.Ala117Pro missense_variant 0.68 pyrazinamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.3 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.25 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 3840264 p.Ile386Thr missense_variant 0.3 cycloserine
alr 3841006 p.Asp139His missense_variant 0.72 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.74 pyrazinamide Not assoc w R
glpK 4138377 p.Val460Ala missense_variant 0.37 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 4139183 c.572dupG frameshift_variant 0.29 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4238941 c.-922G>A upstream_gene_variant 0.3 ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.34 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.22 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243570 p.Thr113Arg missense_variant 0.27 ethambutol Uncertain significance
embA 4244220 c.988C>T synonymous_variant 0.27 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.25 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.34 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.32 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.3 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.31 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.34 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.3 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.31 ethionamide 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 0.28 streptomycin Not assoc w R
gid 4408034 p.Glu57Lys missense_variant 0.27 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.67 streptomycin Not assoc w R