TB-Profiler result

Run: ERR11043789
Summary

Run ID: ERR11043789

Sample name:

Date: 31-03-2023 11:41:07

Number of reads: 7973402

Percentage reads mapped: 99.47

Strain: lineage4.2.1.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 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
rpsL 781822 p.Lys88Thr missense_variant 0.52 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>C upstream_gene_variant 1.0 pyrazinamide
ald 3087252 c.436_437dupGC frameshift_variant 0.16 cycloserine
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326350 c.1123delT frameshift_variant 1.0 ethionamide, ethionamide
gid 4407851 c.351delG frameshift_variant 0.11 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303754 p.His275Arg missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674276 c.75C>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288881 c.361C>A synonymous_variant 1.0
Rv2752c 3065268 p.Gln308His missense_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086791 c.-29T>G upstream_gene_variant 0.38
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840259 p.Tyr388Asp missense_variant 0.25
rpoA 3878613 c.-106A>C upstream_gene_variant 0.2
rpoA 3878637 c.-130G>C upstream_gene_variant 0.2
ddn 3987092 p.Glu83Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.19
embB 4247014 c.501G>T synonymous_variant 1.0
embB 4247024 p.Pro171Ala missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0