TB-Profiler result

Run: SRR998742
Summary

Run ID: SRR998742

Sample name:

Date: 2024-04-14T13:32:30.451306

Number of reads: 4115883

Percentage reads mapped: 99.23

Median coverage: 93.0

Strain: lineage4.1.3;lineage6.3.1

Spoligotype:

Drug-resistance: MDR-TB

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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 0.18
lineage6.3 West-Africa 2 RD702 0.8
lineage4 Euro-American None 0.18
lineage6.3.1 West-Africa 2 RD702 0.79
lineage6 West-Africa 2 RD702 0.79
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu452Pro Assoc w R
isoniazid inhA c.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin gid p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
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 761161 p.Leu452Pro missense_variant 0.15 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.17 isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
katG 2155168 p.Ser315Thr missense_variant 0.16 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.13 ethambutol Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.2 streptomycin 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 6446 p.Ala403Ser missense_variant 0.83 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 0.89 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
gyrA 9557 c.2256G>C synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9591 p.Gly764Arg missense_variant 0.78 levofloxacin Uncertain significance
moxifloxacin
Rv0010c 13460 c.99T>C synonymous_variant 0.81 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.78 isoniazid Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.79 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.77 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 619628 c.-263G>A upstream_gene_variant 0.82 capreomycin
amikacin
kanamycin
Rv0565c 656432 p.Gly347Ser missense_variant 0.79 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.1 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.8 ethionamide
nusG 734151 c.-103G>C upstream_gene_variant 0.78 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.8 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.76 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.68 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.28 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 0.89 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
rpsL 781421 c.-139C>A upstream_gene_variant 0.17 streptomycin Uncertain significance
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 1302899 c.-32A>G upstream_gene_variant 0.84 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fbiC 1304610 c.1680C>T synonymous_variant 0.24 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
embR 1417554 c.-207C>G upstream_gene_variant 0.81 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.83 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476704 n.3053delC non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674434 p.Val78Ala missense_variant 0.92 ethionamide Uncertain significance
isoniazid 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 0.82 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 0.73 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2102694 p.Val117Ile missense_variant 0.83 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.85 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 0.9 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.8 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2222852 p.Ala105Thr missense_variant 0.72 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 2288841 p.Ala134Gly missense_variant 0.2 pyrazinamide Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.74 isoniazid
ald 3086728 c.-92C>T upstream_gene_variant 0.85 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
ald 3087084 c.266delA frameshift_variant 0.77 cycloserine
Rv3083 3449781 c.1278G>A synonymous_variant 0.8 ethionamide Not assoc w R - Interim
Rv3236c 3613354 c.-238G>T upstream_gene_variant 0.74 pyrazinamide
lpqB 3623291 c.1620C>A synonymous_variant 0.22 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3624350 c.561G>T synonymous_variant 0.8 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.84 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624660 p.Ala84Gly missense_variant 0.22 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642397 p.Ala288Val missense_variant 0.79 clofazimine
pretomanid
delamanid
rpoA 3877696 p.Thr271Ile missense_variant 0.82 rifampicin Uncertain significance
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 0.53 rifampicin Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.85 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 0.63 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.85 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.78 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 0.25 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.8 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.76 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.74 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.79 ethambutol Not assoc w R
embB 4248478 c.1965G>A synonymous_variant 0.76 ethambutol
aftB 4268477 c.360C>T synonymous_variant 0.82 ethambutol Not assoc w R - Interim
ubiA 4269351 c.483C>T synonymous_variant 0.77 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.78 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.8 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.81 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.79 ethionamide Uncertain significance
whiB6 4338478 p.Phe15Ser missense_variant 0.75 capreomycin
amikacin
kanamycin
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 4338661 c.-140C>T upstream_gene_variant 0.13 capreomycin
amikacin
kanamycin
whiB6 4338732 c.-211C>T upstream_gene_variant 0.98 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.76 streptomycin Not assoc w R