TB-Profiler result

Run: ERR369620
Summary

Run ID: ERR369620

Sample name:

Date: 01-04-2023 02:46:43

Number of reads: 4685599

Percentage reads mapped: 99.68

Strain: lineage4.6.2.2;lineage4.2.2

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
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
lineage4.6 Euro-American T;LAM None 0.53
lineage4.2 Euro-American H;T;LAM None 0.47
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.46
lineage4.6.2 Euro-American T;LAM RD726 0.54
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 0.5
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 0.59 isoniazid, ethionamide
katG 2155167 p.Ser315Thr missense_variant 0.46 isoniazid
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
mshA 576077 c.730C>T synonymous_variant 0.44
rpoC 763447 c.78C>T synonymous_variant 0.45
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 0.52
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 0.55
fabG1 1674167 p.Met243Thr missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 0.53
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.52
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066276 c.-85G>A upstream_gene_variant 0.42
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.44
thyX 3067474 p.Pro158Ala missense_variant 0.5
ald 3086742 c.-78A>C upstream_gene_variant 0.45
ald 3086788 c.-32T>C upstream_gene_variant 0.51
Rv3083 3448567 p.His22Asp missense_variant 0.55
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612469 c.648A>G synonymous_variant 0.53
Rv3236c 3612571 c.546C>T synonymous_variant 0.55
Rv3236c 3612910 p.Leu69Phe missense_variant 0.44
embA 4242550 c.-683C>G upstream_gene_variant 0.43
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 0.48
ethR 4326739 c.-810G>C upstream_gene_variant 0.54
ethA 4328004 c.-531C>T upstream_gene_variant 0.6
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407794 p.Arg137Trp missense_variant 0.53
gid 4408464 c.-262G>T upstream_gene_variant 0.47