TB-Profiler result

Run: SRR14802083
Summary

Run ID: SRR14802083

Sample name:

Date: 03-04-2023 12:14:39

Number of reads: 5018515

Percentage reads mapped: 99.39

Strain: lineage4.2.1.1

Drug-resistance: Other

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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 0.99
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.99
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.99
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
gid 4407713 c.489delA frameshift_variant 0.97 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 0.98
gyrA 9304 p.Gly668Asp missense_variant 0.97
mshA 576108 p.Ala254Gly missense_variant 0.11
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168561 c.2052T>G synonymous_variant 0.49
PPE35 2169879 p.Phe245Cys missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.53
fbiD 3339744 c.627A>C synonymous_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
rpoA 3877485 c.1023C>T synonymous_variant 1.0
rpoA 3878597 c.-90G>C upstream_gene_variant 0.28
rpoA 3878641 c.-134C>G upstream_gene_variant 0.39
embC 4240409 p.Pro183Ala missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.17
embB 4246529 p.Ser6Arg missense_variant 0.13
embB 4246584 p.Arg24Pro missense_variant 0.17
embB 4248324 p.Ala604Gly missense_variant 0.23
embB 4248328 c.1815G>C synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 0.99