TB-Profiler result

Run: SRR998612
Summary

Run ID: SRR998612

Sample name:

Date: 2024-10-04T12:05:30.660431

Number of reads: 4384260

Percentage reads mapped: 99.26

Median coverage: 98.0

Strain: lineage4.1.3;lineage6.3.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.18
lineage4.1 Euro-American None 0.19
lineage6.3 West-Africa 2 RD702 0.83
lineage4 Euro-American None 0.18
lineage6.3.1 West-Africa 2 RD702 0.8
lineage6 West-Africa 2 RD702 0.83
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 gid c.351delG 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
gid 4407851 c.351delG frameshift_variant 0.2 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 5914 p.Asp225Glu missense_variant 0.22 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6446 p.Ala403Ser missense_variant 0.82 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 9143 c.1842T>C synonymous_variant 0.86 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 0.8 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.8 isoniazid 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 0.81 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 619628 c.-263G>A upstream_gene_variant 0.73 kanamycin
capreomycin
amikacin
ccsA 619862 c.-29G>A upstream_gene_variant 0.86 kanamycin
capreomycin
amikacin
Rv0565c 656432 p.Gly347Ser missense_variant 0.84 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.24 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.78 ethionamide
nusG 734151 c.-103G>C upstream_gene_variant 0.83 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.85 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.8 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.77 rifampicin Not assoc w R
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 0.8 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781421 c.-139C>A upstream_gene_variant 0.21 streptomycin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.83 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 0.94 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fbiC 1304610 c.1680C>T synonymous_variant 0.2 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
embR 1417554 c.-207C>G upstream_gene_variant 0.81 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.84 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674434 p.Val78Ala missense_variant 0.85 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 0.74 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 0.71 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2102694 p.Val117Ile missense_variant 0.77 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.8 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.83 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.87 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.87 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2222852 p.Ala105Thr missense_variant 0.74 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.78 isoniazid
ahpC 2726093 c.-100T>A upstream_gene_variant 0.81 isoniazid
ald 3086728 c.-92C>T upstream_gene_variant 0.72 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
ald 3087084 c.266delA frameshift_variant 0.79 cycloserine
Rv3083 3449781 c.1278G>A synonymous_variant 0.78 ethionamide Not assoc w R - Interim
Rv3236c 3613354 c.-238G>T upstream_gene_variant 0.79 pyrazinamide
lpqB 3624350 c.561G>T synonymous_variant 0.75 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.86 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624660 p.Ala84Gly missense_variant 0.12 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877696 p.Thr271Ile missense_variant 0.77 rifampicin Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.77 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 4138791 p.Ser322Leu missense_variant 0.64 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.84 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.74 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 0.19 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.81 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.79 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 0.72 ethambutol Not assoc w R
aftB 4268477 c.360C>T synonymous_variant 0.86 ethambutol Not assoc w R - Interim
ubiA 4269351 c.483C>T synonymous_variant 0.82 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.86 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.78 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.79 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.79 ethionamide Uncertain significance
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 0.99 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.87 streptomycin Not assoc w R