TB-Profiler result

Run: SRR14781905
Summary

Run ID: SRR14781905

Sample name:

Date: 03-04-2023 11:04:30

Number of reads: 3435139

Percentage reads mapped: 99.68

Strain: lineage4.3.3

Drug-resistance: Sensitive

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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
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.17
mshA 576613 c.1266A>C synonymous_variant 0.28
mshA 576616 c.1269G>C synonymous_variant 0.24
rpoC 764367 p.Gly333Ala missense_variant 0.22
rpoC 764537 p.Pro390Ala missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.19
rpsA 1834836 p.Met432Thr missense_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.99
PPE35 2170045 p.Thr190Pro missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.21
folC 2746340 p.Ala420Val missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.86
fbiD 3339746 p.Ala210Gly missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
whiB7 3568425 c.255T>C synonymous_variant 0.31
whiB7 3568428 c.252A>G synonymous_variant 0.38
whiB7 3568431 c.249C>G synonymous_variant 0.18
rpoA 3878597 c.-90G>C upstream_gene_variant 0.4
rpoA 3878641 c.-134C>G upstream_gene_variant 0.82
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244016 c.784T>C synonymous_variant 0.99
embB 4246527 p.Ala5Gly missense_variant 0.24
embB 4246529 p.Ser6Arg missense_variant 0.41
embB 4246584 p.Arg24Pro missense_variant 0.15
embB 4247020 c.507C>G synonymous_variant 0.2
embB 4248328 c.1815G>C synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0