TB-Profiler result

Run: ERR2517304
Summary

Run ID: ERR2517304

Sample name:

Date: 19-10-2023 23:53:57

Number of reads: 4931164

Percentage reads mapped: 99.61

Strain: lineage4;La1.2.BCG

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide R pncA p.His57Asp (0.60)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
La1 M.bovis None None 0.6
La1.2 M.bovis None None 0.5
lineage4 Euro-American LAM;T;S;X;H None 0.44
La1.2.BCG M.bovis BCG None 0.5
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
pncA 2289073 p.His57Asp missense_variant 0.6 pyrazinamide
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
gyrB 5752 c.513G>A synonymous_variant 0.75
gyrA 6406 c.-896C>T upstream_gene_variant 0.75
gyrB 6446 p.Ala403Ser missense_variant 0.78
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.88
gyrA 8285 c.984C>T synonymous_variant 0.79
gyrA 8624 c.1323G>T synonymous_variant 0.83
gyrA 8741 c.1440C>T synonymous_variant 0.73
gyrA 9143 c.1842T>C synonymous_variant 0.77
gyrA 9304 p.Gly668Asp missense_variant 0.73
fgd1 491742 c.960T>C synonymous_variant 0.6
mshA 576725 p.Ile460Val missense_variant 0.48
rpoC 763031 c.-339T>C upstream_gene_variant 0.58
rpoC 763575 p.Arg69Pro missense_variant 0.58
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.53
mmpL5 776939 c.1542C>T synonymous_variant 0.61
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781568 c.9C>T synonymous_variant 0.61
fbiC 1302899 c.-32A>G upstream_gene_variant 0.5
fbiC 1303638 p.Lys236Asn missense_variant 0.5
embR 1417498 c.-151G>A upstream_gene_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.54
rpsA 1834859 p.Ala440Thr missense_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102106 p.Gly313Arg missense_variant 0.63
ndh 2103173 c.-132delG upstream_gene_variant 0.58
katG 2154724 p.Arg463Leu missense_variant 0.71
katG 2155503 c.609C>T synonymous_variant 0.55
katG 2156025 c.87C>A synonymous_variant 0.51
katG 2156465 c.-354C>T upstream_gene_variant 0.6
PPE35 2167926 p.Leu896Ser missense_variant 0.43
PPE35 2168011 p.Ser868Arg missense_variant 0.56
PPE35 2168149 p.Pro822Ser missense_variant 0.58
PPE35 2168175 p.Gln813Arg missense_variant 0.61
PPE35 2168814 c.1798dupA frameshift_variant 0.5
PPE35 2168920 p.Val565Phe missense_variant 0.48
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.5
ald 3086728 c.-92C>T upstream_gene_variant 0.62
ald 3086788 c.-32T>C upstream_gene_variant 0.57
ald 3087084 c.266delA frameshift_variant 0.46
Rv3083 3448745 p.Ile81Ser missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.53
fprA 3474427 p.Val141Ile missense_variant 0.54
fprA 3475159 p.Asn385Asp missense_variant 0.51
clpC1 4038403 c.2302T>C synonymous_variant 0.6
embC 4240671 p.Thr270Ile missense_variant 0.54
embC 4242029 c.2167C>T synonymous_variant 0.61
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 0.55
embA 4244220 c.988C>T synonymous_variant 0.53
embB 4246551 p.Asn13Ser missense_variant 0.54
embB 4246864 c.351C>T synonymous_variant 0.54
embB 4247173 c.660G>A synonymous_variant 0.57
embB 4247646 p.Glu378Ala missense_variant 0.55
aftB 4267858 p.Ile327Val missense_variant 0.6
aftB 4269351 c.-515C>T upstream_gene_variant 0.68
ubiA 4269387 p.Glu149Asp missense_variant 0.63
aftB 4269606 c.-770T>C upstream_gene_variant 0.56
ubiA 4269689 p.Val49Ile missense_variant 0.61
ubiA 4269864 c.-31C>T upstream_gene_variant 0.43
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.73