TB-Profiler result

Run: ERR1679585
Summary

Run ID: ERR1679585

Sample name:

Date: 31-03-2023 14:54:53

Number of reads: 441054

Percentage reads mapped: 99.77

Strain: lineage4.6.2.2

Drug-resistance: MDR-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 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid
pncA 2288883 p.Leu120Pro missense_variant 0.96 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.36 ethambutol
embB 4247429 p.Met306Val missense_variant 0.4 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
fgd1 490751 c.-32T>G upstream_gene_variant 0.25
ccsA 620794 p.Ala302Thr missense_variant 0.11
rpoB 762477 p.Lys891Glu missense_variant 1.0
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
rplC 801328 c.520C>A synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154991 p.Ser374Tyr missense_variant 0.11
katG 2155389 c.723C>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.27
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
rpoA 3878208 p.Gln100His missense_variant 0.14
embC 4241507 p.Ala549Thr missense_variant 0.17
embC 4241627 p.His589Tyr missense_variant 0.17
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248461 p.Ser650Pro missense_variant 0.12
aftB 4267272 p.Lys522Arg missense_variant 1.0
ubiA 4269298 p.Ile179Ser missense_variant 0.17
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