TB-Profiler result

Run: SRR13180280
Summary

Run ID: SRR13180280

Sample name:

Date: 2024-04-16T00:57:45.739297

Number of reads: 1327355

Percentage reads mapped: 99.27

Median coverage: 68.0

Strain: La1.2;lineage3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.1
La1.2 M.bovis None 0.84
La1 M.bovis None 0.86
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 pncA p.His57Asp Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fbiC c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pncA 2289073 p.His57Asp missense_variant 0.84 pyrazinamide 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
dnaA 467 p.His156Arg missense_variant 0.87 isoniazid Not assoc w R
gyrB 5752 c.513G>A synonymous_variant 0.95 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6406 c.1167C>T synonymous_variant 0.89 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 0.88 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 8285 c.984C>T synonymous_variant 0.87 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8741 c.1440C>T synonymous_variant 0.92 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 0.88 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 13153 p.Ala136Ser missense_variant 0.25 isoniazid Uncertain significance
Rv0010c 13197 p.Thr121Ser missense_variant 0.71 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 0.67 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 0.79 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 574686 c.-662A>G upstream_gene_variant 0.88 ethionamide
isoniazid Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.17 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.82 ethionamide
nusG 734786 p.Arg178His missense_variant 0.87 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.13 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 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 1.0 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 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254582 c.-48A>G upstream_gene_variant 0.85 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.89 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
sigE 1364961 c.549A>C synonymous_variant 0.75 pyrazinamide Not assoc w R - Interim
embR 1417554 c.-207C>G upstream_gene_variant 0.91 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834859 p.Ala440Thr missense_variant 0.92 pyrazinamide 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 0.88 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2102106 p.Gly313Arg missense_variant 0.79 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
ndh 2103173 c.-132delG upstream_gene_variant 0.87 ethionamide
delamanid
isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.87 isoniazid Not assoc w R
katG 2156025 c.87C>A synonymous_variant 0.82 isoniazid Not assoc w R
katG 2156465 c.-354C>T upstream_gene_variant 0.85 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168011 p.Ser868Arg missense_variant 0.93 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 0.86 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.9 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 2289047 c.195C>T synonymous_variant 0.15 pyrazinamide Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.88 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.13 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.13 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2477c 2782927 c.1116A>G synonymous_variant 0.85 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R
amikacin Not assoc w R - Interim
Rv2681 2997325 p.Ala196Val missense_variant 0.82 capreomycin Uncertain significance
ald 3086728 c.-92C>T upstream_gene_variant 0.96 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.83 cycloserine
fbiD 3339154 p.Ile13Leu missense_variant 0.84 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv3083 3448745 p.Ile81Ser missense_variant 0.9 ethionamide Uncertain significance
Rv3083 3448783 p.Val94Ile missense_variant 0.9 ethionamide Uncertain significance
Rv3083 3449318 p.Glu272Ala missense_variant 0.81 ethionamide
lpqB 3623730 p.Ser394Leu missense_variant 0.93 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624350 c.561G>T synonymous_variant 0.91 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.92 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624593 c.318G>A synonymous_variant 0.81 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624710 c.201G>A synonymous_variant 0.85 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877792 p.Ala239Val missense_variant 0.88 rifampicin Uncertain significance
clpC1 4038403 c.2302T>C synonymous_variant 0.87 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.2 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.8 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
embC 4240671 p.Thr270Ile missense_variant 0.93 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.22 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242970 c.3108C>T synonymous_variant 0.88 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.81 ethambutol Not assoc w R
embB 4246551 p.Asn13Ser missense_variant 0.92 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.81 ethambutol Not assoc w R
embB 4247173 c.660G>A synonymous_variant 0.86 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.85 ethambutol Not assoc w R
aftB 4267858 p.Ile327Val missense_variant 0.96 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.88 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.77 ethambutol Not assoc w R
ubiA 4269476 c.358C>T synonymous_variant 0.25 ethambutol Not assoc w R - Interim
ubiA 4269606 c.228T>C synonymous_variant 0.8 ethambutol Not assoc w R
ethA 4326229 c.1245C>T synonymous_variant 0.93 ethionamide Not assoc w R - Interim
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 1.0 streptomycin Not assoc w R