TB-Profiler result

Run: SRR1915479
Summary

Run ID: SRR1915479

Sample name:

Date: 2024-04-16T01:08:32.281642

Number of reads: 2500537

Percentage reads mapped: 87.43

Median coverage: 39.0

Strain: La1.2.BCG

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
La1.2.BCG M.bovis None 1.0
La1.2 M.bovis None 1.0
La1 M.bovis None 1.0
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 1.0 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 0.99 isoniazid Not assoc w R
gyrB 5752 c.513G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6406 c.1167C>T synonymous_variant 0.99 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 1.0 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 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8624 c.1323G>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8741 c.1440C>T synonymous_variant 1.0 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 1.0 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 1.0 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 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
rpoB 763031 c.3225T>C synonymous_variant 0.97 rifampicin Not assoc w R
rpoC 763575 p.Arg69Pro missense_variant 0.98 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
rpsL 781568 c.9C>T synonymous_variant 0.97 streptomycin Not assoc w R
rpsL 781929 p.Gly124Ser missense_variant 0.12 streptomycin Uncertain significance
rpsL 781933 c.374G>A splice_region_variant&stop_retained_variant 0.12 streptomycin
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 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
sigE 1364961 c.549A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473336 n.1491T>G non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473356 n.1511A>G non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833658 c.117C>G synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
rpsA 1833727 c.186G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833730 c.189C>T synonymous_variant 0.14 pyrazinamide
rpsA 1833733 c.192C>T synonymous_variant 0.14 pyrazinamide
rpsA 1833734 p.Ala65Ser missense_variant 0.15 pyrazinamide
rpsA 1833739 c.198C>T synonymous_variant 0.16 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.16 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833778 c.237C>T synonymous_variant 0.19 pyrazinamide
rpsA 1833781 c.240T>G synonymous_variant 0.19 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.21 pyrazinamide
rpsA 1833805 c.264C>T synonymous_variant 0.2 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.19 pyrazinamide
rpsA 1833829 c.288A>G synonymous_variant 0.2 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.2 pyrazinamide
rpsA 1833838 c.297G>A synonymous_variant 0.19 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.19 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.19 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.17 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.19 pyrazinamide
rpsA 1833892 c.351G>A synonymous_variant 0.19 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.17 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.2 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.2 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.19 pyrazinamide
rpsA 1833988 c.447C>T synonymous_variant 0.23 pyrazinamide
rpsA 1833991 c.450C>G synonymous_variant 0.23 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.25 pyrazinamide
rpsA 1834009 c.468C>T synonymous_variant 0.24 pyrazinamide
rpsA 1834012 c.471G>C synonymous_variant 0.22 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.22 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.22 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.23 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.26 pyrazinamide
rpsA 1834096 c.555G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834102 c.561T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
rpsA 1834213 c.672G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834231 c.690T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834234 c.693G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.11 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834294 c.753G>T synonymous_variant 0.18 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.18 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1834357 c.816T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834361 c.820T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
rpsA 1834378 c.837T>C synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
rpsA 1834387 c.846C>T synonymous_variant 0.17 pyrazinamide
rpsA 1834396 c.855G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834859 p.Ala440Thr missense_variant 0.97 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 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 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
ndh 2103173 c.-132delG upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 1.0 isoniazid Not assoc w R
katG 2156025 c.87C>A synonymous_variant 1.0 isoniazid Not assoc w R
katG 2156465 c.-354C>T upstream_gene_variant 1.0 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 1.0 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168920 p.Val565Phe missense_variant 1.0 pyrazinamide Uncertain significance
kasA 2517941 c.-174C>G upstream_gene_variant 0.22 isoniazid
kasA 2517950 c.-165C>G upstream_gene_variant 0.23 isoniazid
kasA 2517959 c.-156C>T upstream_gene_variant 0.24 isoniazid
kasA 2517962 c.-153C>G upstream_gene_variant 0.23 isoniazid
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
Rv2477c 2782928 p.Thr372Lys missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Not assoc w R
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Not assoc w R
amikacin Uncertain significance
Rv2681 2997325 p.Ala196Val missense_variant 1.0 capreomycin Uncertain significance
ald 3086728 c.-92C>T upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
Rv3083 3448783 p.Val94Ile missense_variant 1.0 ethionamide Uncertain significance
lpqB 3623730 p.Ser394Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624350 c.561G>T synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624593 c.318G>A synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624710 c.201G>A synonymous_variant 1.0 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 3878630 c.-124delC upstream_gene_variant 1.0 rifampicin Not assoc w R
clpC1 4038403 c.2302T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 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 4242029 c.2167C>T synonymous_variant 1.0 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 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246551 p.Asn13Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
aftB 4267858 p.Ile327Val missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 1.0 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 1.0 ethambutol 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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R