TB-Profiler result

Run: ERR4799915
Summary

Run ID: ERR4799915

Sample name:

Date: 20-10-2023 03:55:53

Number of reads: 3836078

Percentage reads mapped: 99.45

Strain: lineage4;lineage1.2.2.2

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R ahpC p.Glu76Lys (0.58)
Ethambutol
Pyrazinamide
Streptomycin R gid p.Ser136* (0.12)
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
lineage4 Euro-American LAM;T;S;X;H None 0.51
lineage1 Indo-Oceanic EAI RD239 0.45
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.47
lineage1.2.2.2 Indo-Oceanic NA RD239 0.47
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
ahpC 2726418 p.Glu76Lys missense_variant 0.58 isoniazid
gid 4407796 p.Ser136* stop_gained 0.12 streptomycin
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 5075 c.-165C>T upstream_gene_variant 0.44
gyrB 5115 c.-125G>T upstream_gene_variant 0.47
gyrB 6112 p.Met291Ile missense_variant 0.55
gyrA 7268 c.-34C>T upstream_gene_variant 0.69
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.49
gyrA 8945 c.1644G>A synonymous_variant 0.45
gyrA 9143 c.1842T>C synonymous_variant 0.52
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.59
rpoC 763031 c.-339T>C upstream_gene_variant 0.53
rpoC 763884 p.Ala172Val missense_variant 0.43
rpoC 763886 c.517C>A synonymous_variant 0.42
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.48
mmpS5 779625 c.-720G>A upstream_gene_variant 0.45
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.45
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.47
katG 2154724 p.Arg463Leu missense_variant 0.57
PPE35 2167926 p.Leu896Ser missense_variant 0.57
PPE35 2168742 p.Gly624Asp missense_variant 0.52
Rv1979c 2222308 p.Asp286Gly missense_variant 0.57
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.5
eis 2714581 p.Ala251Gly missense_variant 0.56
ahpC 2726051 c.-142G>A upstream_gene_variant 0.41
folC 2747116 c.483G>A synonymous_variant 0.54
Rv2752c 3065883 c.309C>T synonymous_variant 0.38
ald 3086788 c.-32T>C upstream_gene_variant 0.58
Rv3083 3448714 p.Asp71His missense_variant 0.62
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.49
fprA 3474597 c.591C>A synonymous_variant 0.52
fprA 3475159 p.Asn385Asp missense_variant 0.38
clpC1 4040517 p.Val63Ala missense_variant 0.57
clpC1 4040719 c.-15A>G upstream_gene_variant 0.52
embC 4240671 p.Thr270Ile missense_variant 0.36
embC 4241042 p.Asn394Asp missense_variant 0.37
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.37
embB 4247646 p.Glu378Ala missense_variant 0.38
embB 4249195 c.2682C>T synonymous_variant 0.63
aftB 4267344 p.Val498Ala missense_variant 0.53
aftB 4267960 p.Val293Met missense_variant 0.42
ubiA 4269387 p.Glu149Asp missense_variant 0.6
aftB 4269606 c.-770T>C upstream_gene_variant 0.36
ethA 4326148 c.1326G>T synonymous_variant 0.59
ethA 4326439 p.Asn345Lys missense_variant 0.53
whiB6 4338203 p.Arg107Cys missense_variant 0.53
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.51
gid 4407588 c.615A>G synonymous_variant 0.51
gid 4407775 p.Asp143Ala missense_variant 0.24
gid 4407848 p.Ala119Thr missense_variant 0.43
gid 4407873 c.330G>T synonymous_variant 0.46