TB-Profiler result

Run: SRR6896193
Summary

Run ID: SRR6896193

Sample name:

Date: 04-04-2023 17:58:24

Number of reads: 969589

Percentage reads mapped: 99.17

Strain: lineage4.1.2

Drug-resistance: Other

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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 0.99
lineage4.1.2 Euro-American T;H None 0.98
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
pncA 2289089 p.His51Gln missense_variant 1.0 pyrazinamide
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
fgd1 491591 p.Lys270Met missense_variant 0.94
mshA 576766 c.1419G>A synonymous_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 0.96
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766430 c.3063_3064delTG frameshift_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778134 c.345_346delAC frameshift_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303434 p.Asp168Glu missense_variant 0.93
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674344 p.Gln48Leu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168990 c.1545_1622delGGCGATGACGCCAGCTAACATCACGGTGGGTGCGTTTGATTTGCCGGGGTTGACGGTGCCGTCGTTGACGATTCCAGC disruptive_inframe_deletion 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290171 c.-930G>T upstream_gene_variant 1.0
kasA 2518076 c.-39C>T 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
rpoA 3878498 p.Ser4Pro missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243704 p.Gly158Arg missense_variant 0.11
embB 4245662 c.-852G>A upstream_gene_variant 0.12
embA 4245938 p.Asp902Glu missense_variant 0.1
embB 4248551 p.Ala680Thr missense_variant 1.0
aftB 4268583 c.253dupG frameshift_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408082 p.Val41Ile missense_variant 1.0
PPE35 2168990 c.1544_1622delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT frameshift_variant 1.0