TB-Profiler result

Run: SRR1049960
Summary

Run ID: SRR1049960

Sample name:

Date: 2024-04-16T03:03:54.468487

Number of reads: 6079427

Percentage reads mapped: 98.83

Median coverage: 127.0

Strain: lineage6.3.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage6.3 West-Africa 2 RD702 0.96
lineage6.3.1 West-Africa 2 RD702 0.96
lineage6 West-Africa 2 RD702 0.97
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Ile Assoc w R - Interim High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.96 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin Assoc w R
katG 2155168 p.Ser315Ile missense_variant 0.98 isoniazid Assoc w R - Interim High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.95 ethambutol 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 6446 p.Ala403Ser missense_variant 0.97 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 0.96 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 9591 p.Gly764Arg missense_variant 0.96 levofloxacin Uncertain significance
moxifloxacin
Rv0010c 13460 c.99T>C synonymous_variant 0.93 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.96 isoniazid Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.9 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.93 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 619628 c.-263G>A upstream_gene_variant 0.97 capreomycin
amikacin
kanamycin
Rv0565c 656432 p.Gly347Ser missense_variant 0.97 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.97 ethionamide
nusG 734151 c.-103G>C upstream_gene_variant 0.97 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.96 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.96 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.94 rifampicin Not assoc w R
rpoC 764918 p.Val517Leu missense_variant 0.5 rifampicin Uncertain significance
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 0.94 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.95 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 0.97 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.98 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.98 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471736 n.-110T>C upstream_gene_variant 0.96 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674434 p.Val78Ala missense_variant 0.96 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 0.95 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 0.98 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 0.93 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.97 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.96 isoniazid Not assoc w R
katG 2156366 c.-255G>A upstream_gene_variant 0.96 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.96 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.96 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2222852 p.Ala105Thr missense_variant 0.97 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
kasA 2518132 c.18C>T synonymous_variant 0.96 isoniazid
ald 3086728 c.-92C>T upstream_gene_variant 0.95 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.98 cycloserine
Rv3083 3449781 c.1278G>A synonymous_variant 0.96 ethionamide Not assoc w R - Interim
Rv3236c 3613354 c.-238G>T upstream_gene_variant 0.97 pyrazinamide
lpqB 3624350 c.561G>T synonymous_variant 0.93 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.98 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877696 p.Thr271Ile missense_variant 0.96 rifampicin Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.98 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 4138983 p.Val258Gly missense_variant 0.96 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.99 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.89 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.86 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.89 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.91 ethambutol Not assoc w R
aftB 4268477 c.360C>T synonymous_variant 0.94 ethambutol Not assoc w R - Interim
ubiA 4269351 c.483C>T synonymous_variant 0.98 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.97 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.95 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.95 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.93 ethionamide Uncertain significance
whiB6 4338478 p.Phe15Ser missense_variant 0.97 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.88 streptomycin Not assoc w R