TB-Profiler result

Run: SRR14802103
Summary

Run ID: SRR14802103

Sample name:

Date: 03-04-2023 12:15:50

Number of reads: 3400449

Percentage reads mapped: 99.66

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.98 kanamycin, capreomycin, aminoglycosides, amikacin
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 0.99
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.23
rpoC 764367 p.Gly333Ala missense_variant 0.24
rpoC 764995 c.1626C>G synonymous_variant 0.99
mmpL5 775639 p.Ile948Val 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
fabG1 1673558 p.His40Pro missense_variant 0.18
rpsA 1834836 p.Met432Thr missense_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.98
kasA 2519071 p.Asp319Glu missense_variant 0.16
pepQ 2860159 p.Ala87Gly missense_variant 0.28
Rv2752c 3067135 c.-944C>T upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
ald 3087818 p.Cys333Trp missense_variant 0.12
fbiD 3339734 p.Ala206Gly missense_variant 0.4
fbiD 3339749 p.Val211Gly missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.31
whiB7 3568431 c.249C>G synonymous_variant 0.26
rpoA 3878613 c.-106A>C upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.86
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.26
embB 4246529 p.Ser6Arg missense_variant 0.35
embB 4246584 p.Arg24Pro missense_variant 0.17
embB 4248328 c.1815G>C synonymous_variant 0.18
aftB 4268680 p.Glu53Gln missense_variant 1.0
ethA 4327472 c.2T>C start_lost 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407720 c.483C>G synonymous_variant 1.0
gid 4408014 p.Asp63Glu missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0