TB-Profiler result

Run: ERR7911351
Summary

Run ID: ERR7911351

Sample name:

Date: 02-04-2023 06:57:23

Number of reads: 782370

Percentage reads mapped: 99.7

Strain: lineage4.1.2.1

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
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289119 p.Tyr41* stop_gained 1.0 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
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
gyrA 9620 c.2319G>A synonymous_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759759 c.-48T>G upstream_gene_variant 0.13
rpoB 760115 c.309C>T synonymous_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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155177 p.Ala312Gly missense_variant 0.1
PPE35 2169898 p.Ser239Pro missense_variant 0.14
Rv1979c 2222738 p.Gly143Cys missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289399 c.-158C>T upstream_gene_variant 0.11
pncA 2289640 c.-400delA upstream_gene_variant 0.12
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
clpC1 4038921 p.Phe595Cys missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ethA 4327485 c.-12T>C upstream_gene_variant 1.0
whiB6 4338286 c.235delG frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408050 p.Asn51Lys missense_variant 1.0