TB-Profiler result

Run: ERR2706913
Summary

Run ID: ERR2706913

Sample name:

Date: 31-03-2023 23:08:52

Number of reads: 1481709

Percentage reads mapped: 99.7

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) 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
rpoB 761110 p.Asp435Val missense_variant 0.98 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289043 p.Ser67Pro missense_variant 0.38 pyrazinamide
pncA 2289061 p.Thr61Pro missense_variant 0.57 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.98 para-aminosalicylic_acid
thyA 3073801 p.Pro224Leu missense_variant 1.0 para-aminosalicylic_acid
embB 4247723 p.Pro404Ser missense_variant 1.0 ethambutol
gid 4407816 c.386delG frameshift_variant 1.0 streptomycin
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
gyrB 5452 p.Glu71Asp missense_variant 0.37
gyrA 7362 p.Glu21Gln missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471740 n.-106A>T upstream_gene_variant 0.28
rrs 1472042 n.197T>C non_coding_transcript_exon_variant 0.1
rrs 1472081 n.236C>T non_coding_transcript_exon_variant 0.43
rrl 1473577 n.-81A>T upstream_gene_variant 0.5
rrl 1473663 n.6A>T non_coding_transcript_exon_variant 0.22
rrl 1475957 n.2300A>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168657 c.1956T>A synonymous_variant 0.27
rpoA 3878490 c.18C>G synonymous_variant 0.67
ubiA 4269124 p.Ala237Val missense_variant 0.59
ubiA 4269719 p.Ala39Ser missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0