TB-Profiler result

Run: ERR2514035
Summary

Run ID: ERR2514035

Sample name:

Date: 31-03-2023 20:04:21

Number of reads: 1202531

Percentage reads mapped: 64.72

Strain: lineage3.1.2

Drug-resistance: Other

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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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.21 streptomycin
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620175 c.285C>T synonymous_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761630 c.1824G>A synonymous_variant 0.15
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406293 p.Gly350Arg missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.2
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.2
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.2
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.22
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.33
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.33
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.4
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.5
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.67
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.18
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.23
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.23
rrs 1472846 n.1001C>A non_coding_transcript_exon_variant 0.17
rrl 1473916 n.259C>T non_coding_transcript_exon_variant 0.25
rrl 1474059 n.402C>T non_coding_transcript_exon_variant 0.22
rrl 1474665 n.1008A>T non_coding_transcript_exon_variant 0.12
rrl 1475015 n.1358C>A non_coding_transcript_exon_variant 0.5
rrl 1475774 n.2117C>T non_coding_transcript_exon_variant 0.14
rrl 1475800 n.2143C>T non_coding_transcript_exon_variant 0.14
rrl 1476289 n.2632C>T non_coding_transcript_exon_variant 0.15
rrl 1476403 n.2746G>A non_coding_transcript_exon_variant 0.29
rrl 1476550 n.2893G>A non_coding_transcript_exon_variant 0.25
inhA 1674981 c.780C>A synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918696 p.Ala253Pro missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155914 c.198G>A synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 0.97
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2170150 p.His155Asn missense_variant 0.15
Rv1979c 2223257 c.-93G>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518624 c.510C>T synonymous_variant 0.14
kasA 2518896 p.Pro261Leu missense_variant 0.14
kasA 2519164 c.1050C>T synonymous_variant 0.29
eis 2714992 p.Pro114Leu missense_variant 0.13
eis 2715432 c.-100C>T upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726672 p.Glu160Asp missense_variant 0.1
folC 2746837 c.762G>A synonymous_variant 0.14
pepQ 2860037 p.Val128Met missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475052 p.Asn349Thr missense_variant 1.0
fbiB 3642120 p.Asp196Asn missense_variant 0.12
fbiB 3642238 p.Pro235Leu missense_variant 0.13
embC 4240375 c.513G>A synonymous_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243244 c.12C>T synonymous_variant 0.12
embB 4246565 p.Gly18Arg missense_variant 0.14
embB 4246606 c.93C>T synonymous_variant 0.14
embB 4248241 c.1728C>G synonymous_variant 1.0
embB 4249238 p.Ala909Thr missense_variant 0.12
ethR 4327693 p.Asp49Asn missense_variant 1.0
ethA 4328444 c.-971C>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4408147 p.Ala19Val missense_variant 1.0