TB-Profiler result

Run: ERR2179796
Summary

Run ID: ERR2179796

Sample name:

Date: 15-08-2022 11:53:53

Number of reads: 2878462

Percentage reads mapped: 83.37

Strain: lineage4.2.2

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
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 0.96 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
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 576077 c.730C>T synonymous_variant 1.0
rpoB 761703 p.Gly633Ser missense_variant 1.0
rpoC 764817 p.Val483Ala missense_variant 0.33
rpoC 765462 p.Asn698Ser missense_variant 0.57
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471651 n.-195G>A upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834955 p.Ala472Ser missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612469 c.648A>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243998 p.Ala256Thr missense_variant 1.0
ethA 4328331 c.-858C>T upstream_gene_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>G upstream_gene_variant 0.13
gid 4407731 p.Arg158* stop_gained 1.0