TB-Profiler result

Run: ERR11050362
Summary

Run ID: ERR11050362

Sample name:

Date: 03-04-2023 00:44:24

Number of reads: 4046263

Percentage reads mapped: 99.64

Strain: lineage4.3.4.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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 8715 p.Pro472Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.2
mshA 576108 p.Ala254Gly missense_variant 0.19
mshA 576616 c.1269G>C synonymous_variant 0.25
rpoB 759608 c.-199C>T upstream_gene_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.32
rpoC 764752 c.1383G>C synonymous_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.19
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 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102817 p.Leu76Val missense_variant 0.17
PPE35 2170065 p.Ala183Gly missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.34
ahpC 2726323 p.Pro44Arg missense_variant 1.0
pepQ 2859830 p.Gly197Arg missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
fbiD 3339751 p.Ala212Pro missense_variant 0.27
Rv3083 3448598 p.Ile32Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612768 p.Ala117Pro missense_variant 0.99
rpoA 3878590 c.-83G>C upstream_gene_variant 0.2
rpoA 3878597 c.-90G>C upstream_gene_variant 0.38
rpoA 3878613 c.-106A>C upstream_gene_variant 1.0
rpoA 3878639 c.-132C>G upstream_gene_variant 0.4
rpoA 3878641 c.-134C>G upstream_gene_variant 0.74
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.55
embB 4246584 p.Arg24Pro missense_variant 0.17
embB 4247016 p.Ser168Trp missense_variant 0.21
embB 4248328 c.1815G>C synonymous_variant 0.23
whiB6 4338200 p.Asp108His missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407955 p.Arg83Pro missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0