TB-Profiler result

Run: ERR2515413
Summary

Run ID: ERR2515413

Sample name:

Date: 31-03-2023 20:55:26

Number of reads: 550308

Percentage reads mapped: 99.62

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.99
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576735 p.Leu463Pro missense_variant 0.1
rpoB 759697 c.-110A>T upstream_gene_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 766983 p.Pro1205Gln missense_variant 0.11
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 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.57
Rv1258c 1406956 p.Pro129Ala missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.1
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.1
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.11
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.11
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.1
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.1
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.1
rrs 1472609 n.764G>T non_coding_transcript_exon_variant 0.1
rrl 1473488 n.-170A>G upstream_gene_variant 0.1
rrl 1473608 n.-50G>C upstream_gene_variant 0.11
rrl 1473736 n.83dupG non_coding_transcript_exon_variant 0.18
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 2168644 p.Phe657Leu missense_variant 1.0
PPE35 2169850 p.Asn255Asp missense_variant 0.12
PPE35 2170461 p.Gly51Glu missense_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 2289396 c.-155T>G upstream_gene_variant 0.17
kasA 2518137 p.Asn8Ser missense_variant 0.12
kasA 2519315 p.Ser401Pro missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859539 c.880C>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 0.95
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642483 p.Trp317Arg missense_variant 0.22
rpoA 3878471 p.Val13Ile missense_variant 0.12
ddn 3987034 p.Leu64His missense_variant 0.12
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 0.93
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245862 p.Ile877Asn missense_variant 0.12
embB 4246082 c.-432T>G upstream_gene_variant 0.12
embB 4246801 c.288G>A synonymous_variant 0.12
ubiA 4269128 p.Trp236Arg missense_variant 0.11
ethA 4327220 p.Val85Asp missense_variant 0.11
ethA 4327411 p.Trp21Cys missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0