TB-Profiler result

Run: ERR3014593

Summary

Run ID: ERR3014593

Sample name:

Date: 11-08-2022 22:30:29

Number of reads: 2984594

Percentage reads mapped: 99.5

Strain: lineage4.3.1

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 0.99
lineage4.3.1 Euro-American (LAM) LAM9 None 0.99
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
gyrB 6620 p.Asp461Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289057 p.Pro62Leu missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.98 kanamycin, amikacin
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4327367 c.106delG frameshift_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762745 p.Gln980Arg missense_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766487 p.Pro1040Ser missense_variant 0.18
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
rrl 1475317 n.1660G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102705 c.330_337delCCCCTACG frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087856 p.His346Pro missense_variant 0.94
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878417 p.Gly31Ser missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C upstream_gene_variant 0.37
gid 4408061 p.His48Tyr missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0