TB-Profiler result

Run: ERR161071
Summary

Run ID: ERR161071

Sample name:

Date: 20-10-2023 22:08:14

Number of reads: 7198446

Percentage reads mapped: 99.38

Strain: lineage3;La1.1

Drug-resistance: Sensitive

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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
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 0.14
La1.1 M.bovis None None 0.14
lineage3 East-African-Indian CAS RD750 0.86
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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 0.16
gyrA 8660 c.1359C>T synonymous_variant 0.15
gyrA 9143 c.1842T>C synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.99
rpoB 759746 c.-61C>T upstream_gene_variant 0.85
rpoC 762434 c.-936T>G upstream_gene_variant 0.86
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766582 c.3213C>A synonymous_variant 0.89
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 778066 p.Ala139Thr missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781517 c.-43C>T upstream_gene_variant 0.13
fbiC 1302899 c.-32A>G upstream_gene_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472437 n.592T>G non_coding_transcript_exon_variant 0.13
rrl 1476704 n.3053dupC non_coding_transcript_exon_variant 0.15
fabG1 1673254 c.-186A>C upstream_gene_variant 0.1
rpsA 1834859 p.Ala440Thr missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 0.99
ndh 2103173 c.-132delG upstream_gene_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 0.99
katG 2155503 c.609C>T synonymous_variant 0.14
katG 2156025 c.87C>A synonymous_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2168011 p.Ser868Arg missense_variant 0.15
PPE35 2168814 c.1798dupA frameshift_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.81
pncA 2289365 c.-125delC upstream_gene_variant 0.88
kasA 2518132 c.18C>T synonymous_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 0.81
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.15
Rv3083 3448783 p.Val94Ile missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
fprA 3474427 p.Val141Ile missense_variant 0.11
fprA 3475159 p.Asn385Asp missense_variant 0.15
alr 3841473 c.-53G>A upstream_gene_variant 0.87
alr 3841559 c.-139C>T upstream_gene_variant 0.86
rpoA 3878568 c.-61G>A upstream_gene_variant 0.15
clpC1 4038596 c.2109A>G synonymous_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 0.17
embC 4241975 p.Gln705Glu missense_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 0.18
embB 4247270 p.Leu253Ile missense_variant 0.81
embB 4247646 p.Glu378Ala missense_variant 0.18
embB 4249251 p.Ala913Val missense_variant 0.86
aftB 4267858 p.Ile327Val missense_variant 0.11
aftB 4269351 c.-515C>T upstream_gene_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 0.14
aftB 4269606 c.-770T>C upstream_gene_variant 0.13
whiB6 4338365 p.Cys53Arg missense_variant 0.82
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0