TB-Profiler result

Run: ERR163947
Summary

Run ID: ERR163947

Sample name:

Date: 20-10-2023 22:13:04

Number of reads: 2721880

Percentage reads mapped: 99.16

Strain: lineage1.2.2.2;lineage1.1.2

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.His445Asn (0.47)
Isoniazid R inhA p.Ser94Ala (0.48)
Ethambutol
Pyrazinamide
Streptomycin R rrs n.514A>T (0.27)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R inhA p.Ser94Ala (0.48)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 0.97
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.51
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.49
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.44
lineage1.2.2.2 Indo-Oceanic NA RD239 0.48
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
rpoB 761139 p.His445Asn missense_variant 0.47 rifampicin
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 0.27 streptomycin
inhA 1674481 p.Ser94Ala missense_variant 0.48 isoniazid, ethionamide
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 0.29
gyrB 6112 p.Met291Ile missense_variant 0.98
gyrB 6124 c.885C>T synonymous_variant 0.61
gyrA 7268 c.-34C>T upstream_gene_variant 0.31
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.97
gyrA 9143 c.1842T>C synonymous_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.97
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
rpoC 763552 c.183C>T synonymous_variant 0.44
rpoC 763790 p.Glu141Lys missense_variant 0.68
rpoC 763884 p.Ala172Val missense_variant 0.95
rpoC 763886 c.517C>A synonymous_variant 0.93
rpoC 765171 p.Pro601Leu missense_variant 0.57
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779625 c.-720G>A upstream_gene_variant 0.44
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
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 0.38
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155746 c.366C>T synonymous_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.56
PPE35 2168742 p.Gly624Asp missense_variant 0.59
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.98
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.98
fprA 3474700 p.Gly232Ser missense_variant 0.52
fprA 3475159 p.Asn385Asp missense_variant 0.91
clpC1 4038328 p.Glu793Gln missense_variant 0.45
clpC1 4040517 p.Val63Ala missense_variant 0.97
clpC1 4040719 c.-15A>G upstream_gene_variant 0.4
embC 4240671 p.Thr270Ile missense_variant 0.99
embC 4241042 p.Asn394Asp missense_variant 0.97
embA 4242559 c.-674G>A upstream_gene_variant 0.62
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.48
embA 4245670 p.Ala813Gly missense_variant 0.48
embA 4245969 p.Pro913Ser missense_variant 0.97
embB 4246979 p.Gly156Cys missense_variant 0.56
embB 4247646 p.Glu378Ala missense_variant 0.92
embB 4249654 p.His1047Gln missense_variant 0.6
embB 4249673 p.Ser1054Pro missense_variant 0.53
aftB 4267960 p.Val293Met missense_variant 0.38
ubiA 4269162 p.Leu224Phe missense_variant 0.39
ubiA 4269387 p.Glu149Asp missense_variant 0.97
aftB 4269606 c.-770T>C upstream_gene_variant 0.94
ethA 4326148 c.1326G>T synonymous_variant 0.49
ethA 4326439 p.Asn345Lys missense_variant 0.37
ethA 4328209 c.-736C>A upstream_gene_variant 0.67
whiB6 4338203 p.Arg107Cys missense_variant 0.59
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.98
gid 4407848 p.Ala119Thr missense_variant 0.41
gid 4407873 c.330G>T synonymous_variant 0.97
gid 4407935 p.Leu90Val missense_variant 0.62
gid 4407944 p.Gln87Glu missense_variant 0.65