TB-Profiler result

Run: SRR14782477
Summary

Run ID: SRR14782477

Sample name:

Date: 03-04-2023 11:27:10

Number of reads: 2033186

Percentage reads mapped: 99.48

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 1.0 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
gyrA 9647 c.2346C>G synonymous_variant 0.16
mshA 576456 p.Val370Gly missense_variant 0.35
mshA 576613 c.1266A>C synonymous_variant 0.29
mshA 576616 c.1269G>C synonymous_variant 0.24
rpoC 764367 p.Gly333Ala missense_variant 0.25
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 0.27
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
folC 2747645 c.-47G>A upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.25
Rv2752c 3066171 c.20delC frameshift_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.15
fbiD 3339734 p.Ala206Gly missense_variant 0.56
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.36
whiB7 3568431 c.249C>G synonymous_variant 0.24
rpoA 3877485 c.1023C>T synonymous_variant 0.98
rpoA 3878597 c.-90G>C upstream_gene_variant 0.44
rpoA 3878637 c.-130G>C upstream_gene_variant 0.5
embC 4240409 p.Pro183Ala missense_variant 0.43
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.4
embB 4246584 p.Arg24Pro missense_variant 0.25
embB 4248328 c.1815G>C synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 0.97