TB-Profiler result

Run: ERR2516404
Summary

Run ID: ERR2516404

Sample name:

Date: 31-03-2023 21:31:03

Number of reads: 1701184

Percentage reads mapped: 99.67

Strain: lineage4.3.2

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
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 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
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
gyrA 7570 p.Ala90Val missense_variant 0.89 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
pncA 2288719 p.Met175Val missense_variant 0.12 pyrazinamide
pncA 2289097 p.Asp49Asn missense_variant 0.93 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764817 p.Val483Ala missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472732 n.887G>A non_coding_transcript_exon_variant 0.11
rrs 1473304 n.1459C>T non_coding_transcript_exon_variant 0.2
rrl 1473910 n.253A>G non_coding_transcript_exon_variant 0.25
rrl 1475221 n.1564C>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154022 p.Val697Ala missense_variant 1.0
katG 2155787 p.Ala109Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.31
Rv2752c 3066363 c.-172G>A upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474635 p.Leu210Ser missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269691 p.Tyr48Phe missense_variant 1.0
ethA 4326426 p.Gly350Ser missense_variant 0.24
ethA 4327304 p.Ser57Phe missense_variant 0.87
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407993 p.Ser70Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0