TB-Profiler result

Run: ERR4796880
Summary

Run ID: ERR4796880

Sample name:

Date: 01-04-2023 07:10:16

Number of reads: 4183224

Percentage reads mapped: 99.59

Strain: lineage4.4.1.2

Drug-resistance: HR-TB

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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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.2 Euro-American T1 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 0.19
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 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2156160 c.-49T>C upstream_gene_variant 1.0
PPE35 2167770 p.Ser948Ile missense_variant 0.99
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.32
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860213 p.Pro69Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.63
fbiD 3339744 c.627A>T synonymous_variant 0.33
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878597 c.-90G>C upstream_gene_variant 0.38
rpoA 3878613 c.-106A>C upstream_gene_variant 0.56
rpoA 3878641 c.-134C>G upstream_gene_variant 0.4
embC 4240409 p.Pro183Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 0.42
embB 4246556 p.Ala15Pro missense_variant 0.42
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.36
embB 4249012 c.2499G>A synonymous_variant 1.0
ubiA 4269491 p.Ala115Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407786 c.417G>T synonymous_variant 1.0
gid 4407931 p.Leu91Arg missense_variant 1.0