TB-Profiler result

Run: SRR5073947
Summary

Run ID: SRR5073947

Sample name:

Date: 21-10-2023 04:51:06

Number of reads: 3771468

Percentage reads mapped: 99.4

Strain: lineage4.5;lineage1.1.1.1

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 fabG1 c.-15C>T (0.90), inhA p.Ile21Thr (0.94)
Ethambutol
Pyrazinamide
Streptomycin R gid c.115delC (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.90), inhA p.Ile21Thr (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
lineage4 Euro-American LAM;T;S;X;H None 0.94
lineage1 Indo-Oceanic EAI RD239 0.06
lineage4.5 Euro-American H;T RD122 0.9
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.07
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 0.07
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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.9 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 0.94 isoniazid, ethionamide
gid 4408087 c.115delC frameshift_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 0.84
gyrA 9143 c.1842T>C synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 0.89
rpoC 765171 p.Pro601Leu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302778 c.-153G>A upstream_gene_variant 0.88
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155751 p.Gly121Ser missense_variant 0.92
PPE35 2167926 p.Leu896Ser missense_variant 0.11
PPE35 2167983 p.Gly877Asp missense_variant 0.12
PPE35 2170568 p.Ile15Met missense_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.19
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878336 p.Gly58Arg missense_variant 0.91
clpC1 4038318 p.Pro796Leu missense_variant 0.88
embC 4242095 p.Ala745Thr missense_variant 0.89
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.11
whiB6 4338242 p.Gln94Glu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0