TB-Profiler result

Run: SRR7517702
Summary

Run ID: SRR7517702

Sample name:

Date: 04-04-2023 19:32:46

Number of reads: 1379516

Percentage reads mapped: 98.89

Strain: lineage4.6.2.2

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 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
mshA 576465 p.Ala373Glu missense_variant 0.18
mshA 576512 p.Leu389Met missense_variant 0.22
mshA 576542 p.Ala399Ser missense_variant 0.18
rpoC 767056 c.3687C>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.81
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747558 p.Ala14Asp missense_variant 0.18
pepQ 2859840 p.Ile193Met missense_variant 0.11
thyX 3067271 c.675G>T synonymous_variant 0.18
fbiD 3339248 p.Val44Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038776 p.Glu643Asp missense_variant 0.2
clpC1 4038815 c.1890G>A synonymous_variant 0.2
clpC1 4038848 p.Phe619Leu missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245522 p.Leu764Met missense_variant 0.17
embB 4247017 c.504G>T synonymous_variant 0.21
embB 4248767 p.Asp752His missense_variant 1.0
embB 4248838 c.2325C>A synonymous_variant 0.17
embB 4249734 p.Pro1074His missense_variant 0.29
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407980 p.Pro75Thr missense_variant 1.0