TB-Profiler result

Run: SRR7755725
Summary

Run ID: SRR7755725

Sample name:

Date: 04-04-2023 20:17:06

Number of reads: 3789632

Percentage reads mapped: 99.61

Strain: lineage4.3.3;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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.6
lineage4.2 Euro-American H;T;LAM None 0.34
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.39
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.62
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.38
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 0.32 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 8040 p.Gly247Ser missense_variant 0.78
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.58
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 0.32
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.57
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.63
PPE35 2169879 p.Phe245Cys missense_variant 0.35
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.47
folC 2746340 p.Ala420Val missense_variant 0.63
thyA 3073868 p.Thr202Ala missense_variant 0.61
ald 3086742 c.-78A>C upstream_gene_variant 0.37
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877485 c.1023C>T synonymous_variant 0.41
clpC1 4038287 c.2418C>T synonymous_variant 0.63
clpC1 4038968 c.1737G>A synonymous_variant 0.61
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244539 p.Ala436Val missense_variant 0.56
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.68
gid 4408213 c.-11C>T upstream_gene_variant 0.27