TB-Profiler result

Run: SRR1049598
Summary

Run ID: SRR1049598

Sample name:

Date: 02-04-2023 18:02:27

Number of reads: 4886162

Percentage reads mapped: 98.46

Strain: lineage4.6.1.2

Drug-resistance: RR-TB

Download CSV Download TXT Download PDF Download JSON
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
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 6501 p.Arg421His missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp 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 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.16
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.16
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.16
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.19
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.16
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.13
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.1
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.1
inhA 1674465 c.264C>T synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154874 p.Tyr413Cys missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 0.99
ethR 4328183 p.Tyr212Cys missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0