TB-Profiler result

Run: ERR3287777
Summary

Run ID: ERR3287777

Sample name:

Date: 01-04-2023 01:39:28

Number of reads: 4232446

Percentage reads mapped: 99.78

Strain: lineage4.9;lineage4.3.4.1

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 0.89
lineage4.9 Euro-American (H37Rv-like) T1 None 0.09
lineage4.3.4 Euro-American (LAM) LAM RD174 0.9
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.9
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 761108 p.Met434Ile missense_variant 0.85 rifampicin
rpoB 761110 p.Asp435Gly missense_variant 0.86 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.89 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 0.86
gyrA 7585 p.Ser95Thr missense_variant 0.89
gyrA 9304 p.Gly668Asp missense_variant 0.9
rpoB 761167 p.Pro454Leu missense_variant 0.89
rpoC 764995 c.1626C>G synonymous_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 0.92
rpsL 781395 c.-165T>C upstream_gene_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 0.91
katG 2155787 p.Ala109Thr missense_variant 0.84
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.86
ahpC 2726323 p.Pro44Arg missense_variant 0.89
thyX 3067657 p.Arg97Trp missense_variant 0.93
thyA 3073868 p.Thr202Ala missense_variant 0.9
ald 3086788 c.-32T>C upstream_gene_variant 0.92
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.91
Rv3236c 3612009 p.Ala370Thr missense_variant 0.86
Rv3236c 3612896 p.Gly74Ala missense_variant 0.89
clpC1 4038287 c.2418C>T synonymous_variant 0.9
embA 4242643 c.-590C>T upstream_gene_variant 0.88
embB 4248320 p.Gly603Arg missense_variant 0.82
ubiA 4269721 p.Ala38Val missense_variant 0.89
ethA 4327311 p.Ser55Ala missense_variant 0.9
whiB6 4338595 c.-75delG upstream_gene_variant 0.94
gid 4407831 c.371dupT frameshift_variant 0.88
gid 4408156 p.Leu16Arg missense_variant 0.92