TB-Profiler result

Run: ERR11043556

Summary

Run ID: ERR11043556

Sample name:

Date: 31-03-2023 11:36:41

Number of reads: 3707181

Percentage reads mapped: 99.55

Strain: lineage4.1.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.2 Euro-American (X-type) X1 None 1.0
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 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.18
mshA 576456 p.Val370Gly missense_variant 0.28
mshA 576606 p.Ala420Gly missense_variant 0.24
mshA 576613 c.1266A>C synonymous_variant 0.25
mshA 576616 c.1269G>C synonymous_variant 0.36
rpoC 764367 p.Gly333Ala missense_variant 0.27
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.3
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471771 n.-74delG upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169522 p.Ala364Val missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.32
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.27
pepQ 2860159 p.Ala87Gly missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.47
fbiD 3339746 p.Ala210Gly missense_variant 0.4
fbiD 3339749 p.Val211Gly missense_variant 0.17
fbiD 3339751 p.Ala212Pro missense_variant 0.17
Rv3083 3449787 c.1284C>T synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878590 c.-83G>C upstream_gene_variant 0.25
rpoA 3878597 c.-90G>C upstream_gene_variant 0.67
rpoA 3878637 c.-130G>C upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.52
embC 4240409 p.Pro183Ala missense_variant 0.34
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243833 p.Ala201Thr missense_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.52
embB 4246584 p.Arg24Pro missense_variant 0.25
embB 4246930 p.Gln139His missense_variant 1.0
embB 4247016 p.Ser168Trp missense_variant 0.23
embB 4247020 c.507C>G synonymous_variant 0.17
embB 4248328 c.1815G>C synonymous_variant 0.21
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4268900 c.-64C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0