TB-Profiler result

Run: ERR278516
Summary

Run ID: ERR278516

Sample name:

Date: 31-03-2023 23:32:56

Number of reads: 4944541

Percentage reads mapped: 99.52

Strain: lineage4.6.1.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.2 Euro-American T2 RD724 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 761140 p.His445Arg missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 7539 p.Thr80Ala missense_variant 1.0
gyrA 7570 p.Ala90Gly missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764810 p.Pro481Thr missense_variant 1.0
rpoC 765065 p.Leu566Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472029 n.184C>T non_coding_transcript_exon_variant 0.14
rrs 1472469 n.624G>A non_coding_transcript_exon_variant 0.22
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.33
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.13
rrl 1474165 n.508G>T non_coding_transcript_exon_variant 0.17
rrl 1474339 n.682C>T non_coding_transcript_exon_variant 0.15
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.12
rrl 1475120 n.1463G>A non_coding_transcript_exon_variant 0.25
rrl 1475214 n.1557G>A non_coding_transcript_exon_variant 0.25
rrl 1475373 n.1716G>A non_coding_transcript_exon_variant 1.0
rrl 1475560 n.1903A>G non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065920 p.Pro91Leu missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987215 c.372A>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 1.0
ethA 4326572 p.Leu301Pro missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0