TB-Profiler result

Run: ERR4799359
Summary

Run ID: ERR4799359

Sample name:

Date: 20-10-2023 03:34:34

Number of reads: 3412477

Percentage reads mapped: 99.42

Strain: lineage1.2.2.2

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.Leu430Pro (0.93), rpoB p.His445Asn (0.83)
Isoniazid R fabG1 c.-15C>T (1.00), inhA p.Ser94Ala (0.94)
Ethambutol R embA c.-12C>T (0.96), embB p.Met306Ile (0.97)
Pyrazinamide R pncA p.His71Pro (0.99)
Streptomycin R rrs n.514A>C (0.97)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1401A>G (0.96)
Amikacin R rrs n.1401A>G (0.96)
Capreomycin R rrs n.1401A>G (0.96)
Kanamycin R rrs n.1401A>G (0.96)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), inhA p.Ser94Ala (0.94)
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
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.99
lineage1.2.2.2 Indo-Oceanic NA RD239 0.98
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 761095 p.Leu430Pro missense_variant 0.93 rifampicin
rpoB 761139 p.His445Asn missense_variant 0.83 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.97 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.96 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 0.94 isoniazid, ethionamide
pncA 2289030 p.His71Pro missense_variant 0.99 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.96 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.97 ethambutol
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 0.98
gyrB 6112 p.Met291Ile missense_variant 0.97
gyrA 7268 c.-34C>T upstream_gene_variant 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.98
gyrA 9143 c.1842T>C synonymous_variant 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763884 p.Ala172Val missense_variant 0.96
rpoC 763886 c.517C>A synonymous_variant 0.97
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpS5 779625 c.-720G>A upstream_gene_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.97
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 0.97
katG 2154724 p.Arg463Leu missense_variant 0.98
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.98
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.99
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 0.99
clpC1 4040719 c.-15A>G upstream_gene_variant 0.98
embC 4240671 p.Thr270Ile missense_variant 0.97
embC 4241042 p.Asn394Asp missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.99
embB 4247646 p.Glu378Ala missense_variant 0.98
aftB 4267960 p.Val293Met missense_variant 0.97
ubiA 4269387 p.Glu149Asp missense_variant 0.95
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 0.96
ethA 4326439 p.Asn345Lys missense_variant 0.99
whiB6 4338203 p.Arg107Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.99
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407848 p.Ala119Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0