TB-Profiler result

Run: ERR4423594
Summary

Run ID: ERR4423594

Sample name:

Date: 01-04-2023 05:54:47

Number of reads: 316321

Percentage reads mapped: 99.57

Strain: lineage4.1

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
lineage4.1 Euro-American T;X;H 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 761139 p.His445Asp missense_variant 1.0 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289219 p.Asp8Ala missense_variant 1.0 pyrazinamide
gid 4407967 p.Leu79Ser missense_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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8570 p.Glu423Asp missense_variant 0.12
gyrA 9282 p.Gly661Cys missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9557 c.2256G>C synonymous_variant 1.0
gyrA 9614 p.Asp771Glu missense_variant 0.5
fgd1 491090 p.Leu103His missense_variant 0.22
mshA 576578 p.Gly411Arg missense_variant 0.22
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775883 c.2598C>A synonymous_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
rpsL 781559 c.-1G>C upstream_gene_variant 0.2
fbiC 1304610 c.1680C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473233 n.1388C>A non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169912 p.Asn234Ser missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746825 c.774G>A synonymous_variant 0.18
folC 2746832 p.Val256Gly missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642012 p.Gln160Lys missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246722 p.Pro70Gln missense_variant 0.29
embB 4246764 p.Pro84Gln missense_variant 0.22
ubiA 4269770 p.Arg22Gly missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0