TB-Profiler result

Run: ERR4817789
Summary

Run ID: ERR4817789

Sample name:

Date: 01-04-2023 15:11:38

Number of reads: 914620

Percentage reads mapped: 99.48

Strain: lineage4.3.1

Drug-resistance: Sensitive

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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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.1 Euro-American (LAM) LAM9 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
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 8014 c.715_716dupGG frameshift_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.34
rpoB 761535 p.Pro577Thr missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765502 c.2133G>A synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778635 p.Thr91Ala missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416426 c.919_921delGCG conservative_inframe_deletion 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.5
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.5
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.5
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.5
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.5
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.5
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.5
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.5
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5
rrl 1473532 n.-126T>C upstream_gene_variant 0.14
rrl 1476007 n.2350T>G non_coding_transcript_exon_variant 1.0
fabG1 1673560 p.Lys41Leu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156404 c.-293G>A upstream_gene_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.27
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.11
PPE35 2170153 c.459delC frameshift_variant 0.11
Rv1979c 2222936 p.Ala77Thr missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289503 c.-262G>T upstream_gene_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449041 p.Val180Ile missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475206 p.Glu400Asp missense_variant 0.1
whiB7 3568757 c.-78A>G upstream_gene_variant 1.0
rpoA 3878578 c.-71C>A upstream_gene_variant 0.67
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039042 p.Ser555Thr missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249787 p.Gly1092Ser missense_variant 0.11
aftB 4268393 c.444G>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0