TB-Profiler result

Run: SRR998850
Summary

Run ID: SRR998850

Sample name:

Date: 04-04-2023 23:38:59

Number of reads: 1762899

Percentage reads mapped: 99.27

Strain: lineage4.1.3

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 0.99
lineage4.1 Euro-American T;X;H None 0.97
lineage4.1.3 Euro-American T;X;H None 0.94
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.Ser450Phe missense_variant 0.87 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
pncA 2288832 p.His137Arg missense_variant 0.91 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.95 ethambutol
gid 4408100 c.102delG frameshift_variant 0.97 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 0.97
fbiC 1304610 c.1680C>T synonymous_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474235 n.578G>T non_coding_transcript_exon_variant 0.12
inhA 1674102 c.-100C>A upstream_gene_variant 0.85
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156180 c.-69C>T upstream_gene_variant 0.13
katG 2156183 c.-72G>T upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ubiA 4269311 p.Trp175Arg missense_variant 0.13
ubiA 4269313 p.Lys174Thr missense_variant 0.75
ubiA 4269387 p.Glu149Asp missense_variant 0.12
ethA 4327471 c.3G>T start_lost 0.91