TB-Profiler result

Run: ERR2653066
Summary

Run ID: ERR2653066

Sample name:

Date: 31-03-2023 22:28:45

Number of reads: 924545

Percentage reads mapped: 99.4

Strain: lineage4.1.2

Drug-resistance: HR-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 0.99
lineage4.1.2 Euro-American T;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
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid
ethR 4327876 p.Phe110Leu missense_variant 1.0 ethionamide
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 6014 p.Asp259Asn missense_variant 0.11
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 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 763016 p.Met1070Ile missense_variant 1.0
rpoC 764782 c.1413C>T synonymous_variant 0.95
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
rplC 800889 c.81C>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472207 n.362A>G non_coding_transcript_exon_variant 0.11
rrs 1472259 n.414C>T non_coding_transcript_exon_variant 1.0
rrl 1475392 n.1735C>A non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168303 c.2310G>T synonymous_variant 1.0
PPE35 2169776 p.Phe279Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G 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
Rv3236c 3612029 p.Ala363Val missense_variant 0.11
Rv3236c 3612289 c.828G>C synonymous_variant 0.1
alr 3840263 c.1158C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ethA 4326475 c.999G>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0