TB-Profiler result

Run: SRR21689653
Summary

Run ID: SRR21689653

Sample name:

Date: 2024-10-05T00:04:38.332449

Number of reads: 8291452

Percentage reads mapped: 99.98

Median coverage: 91.0

Strain: La1.2.BCG;lineage1.1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1 Indo-Oceanic RD239 0.09
La1.2.BCG M.bovis None 0.9
lineage1 Indo-Oceanic RD239 0.07
lineage1.1.1 Indo-Oceanic RD239 0.09
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
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
pncA 2289073 p.His57Asp missense_variant 0.94 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 0.85 isoniazid Not assoc w R
gyrB 5752 c.513G>A synonymous_variant 0.89 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6112 p.Met291Ile missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6406 c.1167C>T synonymous_variant 0.93 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 0.89 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 0.92 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8624 c.1323G>T synonymous_variant 0.88 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 1.0 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 13197 p.Thr121Ser missense_variant 0.95 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 0.92 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.17 rifampicin Not assoc w R
mmaA3 738149 p.Met1? start_lost 0.18 isoniazid
rpoB 760386 p.His194Tyr missense_variant 0.15 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763575 p.Arg69Pro missense_variant 0.9 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.13 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 1.0 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 781568 c.9C>T synonymous_variant 0.86 streptomycin Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.11 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254582 c.-48A>G upstream_gene_variant 0.89 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.98 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
sigE 1364961 c.549A>C synonymous_variant 0.9 pyrazinamide Not assoc w R - Interim
embR 1417019 p.Cys110Tyr missense_variant 0.12 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834319 p.Val260Ile missense_variant 0.11 pyrazinamide 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 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.13 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 2102106 p.Gly313Arg missense_variant 0.86 isoniazid Not assoc w R - Interim
delamanid Uncertain significance
ethionamide Uncertain significance
ndh 2103173 c.-132delG upstream_gene_variant 0.76 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.81 isoniazid Not assoc w R
katG 2156025 c.87C>A synonymous_variant 0.94 isoniazid Not assoc w R
katG 2156465 c.-354C>T upstream_gene_variant 0.84 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 0.94 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 0.8 pyrazinamide Uncertain significance
PPE35 2168920 p.Val565Phe missense_variant 0.88 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
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 1.0 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.17 isoniazid
ahpC 2726070 c.-123G>A upstream_gene_variant 0.16 isoniazid
Rv2477c 2782928 p.Thr372Lys missense_variant 0.95 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2681 2997325 p.Ala196Val missense_variant 0.85 capreomycin Uncertain significance
Rv2752c 3064632 c.1560C>T synonymous_variant 0.28 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086728 c.-92C>T upstream_gene_variant 0.8 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.91 cycloserine
Rv3083 3448745 p.Ile81Ser missense_variant 0.89 ethionamide Uncertain significance
Rv3083 3448783 p.Val94Ile missense_variant 0.87 ethionamide Uncertain significance
lpqB 3623730 p.Ser394Leu missense_variant 0.9 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3623978 p.Asp311Glu missense_variant 0.88 rifampicin Uncertain significance
bedaquiline Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.95 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624593 c.318G>A synonymous_variant 0.85 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624710 c.201G>A synonymous_variant 0.89 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878630 c.-124delC upstream_gene_variant 1.0 rifampicin Not assoc w R
clpC1 4038403 c.2302T>C synonymous_variant 0.84 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 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.570_572dupGGG disruptive_inframe_insertion 0.82 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4242029 c.2167C>T synonymous_variant 0.94 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242970 c.3108C>T synonymous_variant 0.98 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 0.11 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.91 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.11 ethambutol Not assoc w R
embB 4246551 p.Asn13Ser missense_variant 0.95 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.98 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 1.0 ethambutol Not assoc w R
aftB 4267858 p.Ile327Val missense_variant 0.91 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.93 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269689 p.Val49Ile missense_variant 0.91 ethambutol Not assoc w R - Interim
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 4338603 c.-82C>T upstream_gene_variant 0.13 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 1.0 streptomycin Not assoc w R