TB-Profiler result

Run: ERR2514308
Summary

Run ID: ERR2514308

Sample name:

Date: 31-03-2023 20:15:24

Number of reads: 782423

Percentage reads mapped: 99.4

Strain: lineage3

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
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 0.25 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 8923 p.Gly541Val missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.32
ccsA 620821 p.Asn311Tyr missense_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764181 p.Asp271Gly missense_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
fbiC 1303016 p.Val29Gly missense_variant 0.3
fbiC 1303978 p.Gly350Trp missense_variant 0.17
fbiC 1304260 p.Trp444Arg missense_variant 0.11
fbiC 1304421 c.1491C>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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 1473213 n.1368A>T non_coding_transcript_exon_variant 0.2
rrl 1473515 n.-143G>A upstream_gene_variant 0.14
rrl 1476031 n.2374C>A non_coding_transcript_exon_variant 0.4
rrl 1476787 n.3130C>A non_coding_transcript_exon_variant 0.12
rpsA 1833354 c.-188G>A upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170443 p.Trp57Leu missense_variant 0.12
PPE35 2170769 c.-157C>T 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
pncA 2289492 c.-251C>A upstream_gene_variant 0.25
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.3
ahpC 2726665 p.Val158Ala missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338976 c.-142G>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640546 p.Lys2Glu missense_variant 1.0
clpC1 4039958 c.747G>A synonymous_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243082 c.3221_3228delATCTGAAC frameshift_variant 0.18
embC 4243092 p.Leu1077Arg missense_variant 0.17
embC 4243095 p.Gly1078Val missense_variant 0.17
embA 4243099 c.-134G>C upstream_gene_variant 0.17
embA 4243102 c.-131G>T upstream_gene_variant 0.17
embC 4243103 p.Thr1081Pro missense_variant 0.15
embC 4243106 p.Arg1082Ser missense_variant 0.15
embC 4243107 c.3245_3246insGTTCAGAT frameshift_variant 0.15
embB 4247028 p.Leu172Arg missense_variant 0.14
embB 4249729 c.3216T>C synonymous_variant 0.14
ethR 4326964 c.-585G>A upstream_gene_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0