TB-Profiler result

Run: ERR4813599
Summary

Run ID: ERR4813599

Sample name:

Date: 01-04-2023 12:52:22

Number of reads: 4944173

Percentage reads mapped: 99.83

Strain: lineage4.3.4.2;lineage4.3.3

Drug-resistance: MDR-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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.11
lineage4.3.4 Euro-American (LAM) LAM RD174 0.91
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.89
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
rpoB 761155 p.Ser450Leu missense_variant 0.1 rifampicin
inhA 1674262 p.Ile21Val missense_variant 0.11 isoniazid
pncA 2289090 p.His51Arg missense_variant 0.11 pyrazinamide
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 0.99
gyrA 8040 p.Gly247Ser missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766487 p.Pro1040Ala missense_variant 0.14
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
rpsA 1834683 p.Ala381Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169041 c.1572G>A synonymous_variant 0.26
PPE35 2169044 c.1569G>C synonymous_variant 0.3
PPE35 2169047 p.Ile522Val missense_variant 0.25
PPE35 2169053 c.1560T>C synonymous_variant 0.57
PPE35 2169056 c.1557A>G synonymous_variant 0.24
PPE35 2169059 c.1554G>A synonymous_variant 0.31
PPE35 2169063 p.Met517Thr missense_variant 0.55
PPE35 2169065 p.Ala516Ile missense_variant 0.31
PPE35 2169068 c.1545G>T synonymous_variant 0.33
PPE35 2169071 c.1542A>G synonymous_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474049 p.Ala15Thr missense_variant 0.89
fprA 3474816 c.810G>A synonymous_variant 0.92
Rv3236c 3612009 p.Ala370Thr missense_variant 0.89
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038824 c.1881C>T synonymous_variant 0.88
embC 4242176 p.Pro772Ala missense_variant 0.9
embA 4242643 c.-590C>T upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0