TB-Profiler result

Run: ERR9787095
Summary

Run ID: ERR9787095

Sample name:

Date: 2024-10-04T00:17:22.404987

Number of reads: 3050573

Percentage reads mapped: 99.49

Median coverage: 148.0

Strain: lineage4.1.2.1;lineage6.1.3

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.24
lineage4.1.2 Euro-American None 0.24
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.23
lineage6.1.3 West-Africa 2 RD702 0.56
lineage4 Euro-American None 0.24
lineage6 West-Africa 2 RD702 0.76
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol embC p.Ala307Thr Uncertain significance Mutation from literature
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
embC 4240781 p.Ala307Thr missense_variant 0.84 ethambutol Uncertain significance Mutation from literature
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 5236 c.-4G>T upstream_gene_variant 0.75 levofloxacin
moxifloxacin
gyrB 6446 p.Ala403Ser missense_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 7361 c.60C>T synonymous_variant 0.25 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 0.99 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 7750 p.Val150Ala missense_variant 0.71 levofloxacin
moxifloxacin Uncertain significance
gyrA 8493 p.Leu398Phe missense_variant 0.73 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9143 c.1842T>C synonymous_variant 0.73 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 13460 c.99T>C synonymous_variant 0.7 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.74 isoniazid Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.24 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.78 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.77 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.25 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 656432 p.Gly347Ser missense_variant 0.7 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.2 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.72 ethionamide
rpoB 760115 c.309C>T synonymous_variant 0.29 rifampicin Not assoc w R
rpoB 760855 p.Thr350Ile missense_variant 0.71 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.73 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.74 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.82 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.27 rifampicin Not assoc w R
rpoC 766231 c.2862T>C synonymous_variant 0.75 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.68 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.74 streptomycin Not assoc w R
rplC 800232 c.-577G>T upstream_gene_variant 0.79 linezolid
Rv1129c 1254501 p.Thr12Ala missense_variant 0.77 levofloxacin
moxifloxacin
isoniazid
rifampicin
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.76 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.76 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv1258c 1406685 p.Val219Ala missense_variant 0.75 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416633 p.Leu239Val missense_variant 0.77 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.82 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.75 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673952 c.-250G>A upstream_gene_variant 0.7 isoniazid
ethionamide
inhA 1674434 p.Val78Ala missense_variant 0.77 isoniazid Not assoc w R
ethionamide 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 0.72 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063121 c.1608A>T synonymous_variant 0.75 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
bacA 2064135 c.594G>A synonymous_variant 0.8 kanamycin
capreomycin
streptomycin
amikacin
katG 2154724 p.Arg463Leu missense_variant 0.66 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.76 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.74 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.83 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2222694 c.471G>A synonymous_variant 0.23 bedaquiline
clofazimine
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.23 isoniazid
kasA 2518132 c.18C>T synonymous_variant 0.82 isoniazid
ald 3086728 c.-92C>T upstream_gene_variant 0.73 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.79 cycloserine
Rv3236c 3612143 p.Arg325His missense_variant 0.75 pyrazinamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.78 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.73 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627756 c.-407A>T upstream_gene_variant 0.2 rifampicin
bedaquiline
clpC1 4038408 p.Pro766Leu missense_variant 0.24 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.78 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.68 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.21 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.83 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.69 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.15 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.77 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.8 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.8 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.7 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.73 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.7 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.7 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.71 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.79 ethionamide Uncertain significance
ethR 4327981 p.Trp145Arg missense_variant 0.28 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.77 streptomycin Not assoc w R
gid 4408034 p.Glu57Lys missense_variant 0.75 streptomycin Uncertain significance