TB-Profiler result

Run: SRR1162841
Summary

Run ID: SRR1162841

Sample name:

Date: 02-04-2023 23:20:37

Number of reads: 1642798

Percentage reads mapped: 85.57

Strain: lineage4.3.3

Drug-resistance: MDR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.98
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.24 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.95
gyrA 9304 p.Gly668Asp missense_variant 0.91
rpoB 762613 p.Ser936Ile missense_variant 0.12
rpoC 764942 p.His525Asn missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_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
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.14
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.14
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.15
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.16
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.16
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.17
rrs 1472278 n.433C>T non_coding_transcript_exon_variant 0.14
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.13
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.13
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.12
rrs 1472574 n.729T>G non_coding_transcript_exon_variant 0.12
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.15
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.15
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.15
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.17
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.18
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.24
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.24
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.25
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.25
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.17
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.17
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.1
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.15
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.15
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.15
rrs 1473262 n.1417T>G non_coding_transcript_exon_variant 0.15
rrl 1474756 n.1099T>C non_coding_transcript_exon_variant 0.11
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.17
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.17
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.19
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.21
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.21
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.22
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.19
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.19
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.17
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.91
ald 3086788 c.-32T>C upstream_gene_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.98
embC 4242182 p.Ala774Ser missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407905 p.Phe100Val missense_variant 0.97
gid 4408156 p.Leu16Arg missense_variant 1.0