TB-Profiler result

Run: ERR6358871

Summary

Run ID: ERR6358871

Sample name:

Date: 02-04-2023 02:20:34

Number of reads: 6987849

Percentage reads mapped: 99.6

Strain: lineage4.6.1.2

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 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.2 Euro-American T2 RD724 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 760314 p.Val170Phe missense_variant 1.0 rifampicin
katG 2155573 p.Thr180Lys missense_variant 0.99 isoniazid
pncA 2288826 p.Val139Ala missense_variant 0.43 pyrazinamide
pncA 2289016 p.Thr76Pro missense_variant 0.28 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.27 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4408047 p.Cys52* stop_gained 0.99 streptomycin
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 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.27
rpoC 764817 p.Val483Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101786 c.1257G>A synonymous_variant 1.0
PPE35 2170700 c.-88G>A upstream_gene_variant 0.32
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065954 p.Thr80Ala missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878599 c.-92C>G upstream_gene_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.21
embB 4247378 p.Leu289Ile missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0