<div dir="ltr">Hi Nikolas,<div><br></div><div>It appears there's some erroneous data in the cache for rs13346240; the SNP does not appear in the 1000 genomes phase 1 source data, but somehow some frequency data corresponding to that rsID has appeared in the cache files.</div><div><br></div><div>The correct value for the AFR_AF at this locus is C:0.81</div><div><br></div><div>We'll look into making sure this doesn't appear in future versions of the cache.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 31 January 2015 at 14:31, Nikolas Pontikos <span dir="ltr"><<a href="mailto:n.pontikos@ucl.ac.uk" target="_blank">n.pontikos@ucl.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello,<br>
<br>
<br>
<br>
I am getting two very different allele freq returned: C:0.02, C:0.81<br>
for the AFR_MAF field at position 19:5831713<br>
<br>
Please see output in csv format below.<br>
<br>
Could you please explain to me how to interpret these?<br>
<br>
The second one appears to match the freq of the second SNP:<br>
<a href="http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=19:5831213-5832213;source=dbSNP;tl=T6pK51e9LuJlbJfH-577229;v=rs112313064;vdb=variation;vf=24908425" target="_blank">http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=19:5831213-5832213;source=dbSNP;tl=T6pK51e9LuJlbJfH-577229;v=rs112313064;vdb=variation;vf=24908425</a><br>
<br>
But I don't see any freq info about the first SNP:<br>
<a href="http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=19:5831213-5832213;tl=T6pK51e9LuJlbJfH-577229;v=rs13346240;vdb=variation;vf=9502280#11943_tablePanel" target="_blank">http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=19:5831213-5832213;tl=T6pK51e9LuJlbJfH-577229;v=rs13346240;vdb=variation;vf=9502280#11943_tablePanel</a><br>
<br>
How is 0.02 estimated?<br>
<br>
Many Thanks,<br>
<br>
<br>
Nikolas.<br>
<br>
<br>
<br>
"Identifier of uploaded variantUploaded variation","Location of<br>
variant in standard coordinate format (chr:start or<br>
chr:start-end)Location","The variant allele used to calculate the<br>
consequenceAllele","Ensembl stable ID of affected geneGene","Ensembl<br>
stable ID of featureFeature","Type of feature - Transcript,<br>
RegulatoryFeature or MotifFeatureFeature type","Consequence<br>
typeConsequence","Relative position of base pair in cDNA sequencecDNA<br>
position","Relative position of base pair in coding sequenceCDS<br>
position","Relative position of amino acid in proteinProtein<br>
position","Reference and variant amino acidsAmino acids","Reference<br>
and variant codon sequenceCodons","Identifier(s) of co-located known<br>
variantsExisting variation","Shortest distance from variant to<br>
transcriptDistance to transcript","Strand of the feature (1/-1)Feature<br>
strand","Gene symbol (e.g. HGNC)Symbol","Source of gene symbolSymbol<br>
source","Stable identifer of HGNC gene symbolHGNC ID","Biotype of<br>
transcript or regulatory featureBiotype","Indicates if transcript is<br>
canonical for this geneCanonical","Transcript support levelTranscript<br>
support level","Indicates if transcript is a CCDS<br>
transcriptCCDS","Ensembl protein identiferENSP","SIFT prediction<br>
and/or scoreSIFT","PolyPhen prediction and/or scorePolyPhen","Exon<br>
number(s) / totalExon","Intron number(s) / totalIntron","The source<br>
and identifer of any overlapping protein domainsDomains","HGVS coding<br>
sequence nameHGVSc","HGVS protein sequence nameHGVSp","Minor allele<br>
and frequency of existing variant in 1000 Genomes Phase 1 combined<br>
populationGMAF","Frequency of existing variant in 1000 Genomes Phase 1<br>
combined African populationAFR MAF","Frequency of existing variant in<br>
1000 Genomes Phase 1 combined American populationAMR MAF","Frequency<br>
of existing variant in 1000 Genomes Phase 1 combined Asian<br>
populationASN MAF","Frequency of existing variant in 1000 Genomes<br>
Phase 1 combined European populationEUR MAF","Frequency of existing<br>
variant in NHLBI-ESP African American populationAA MAF","Frequency of<br>
existing variant in NHLBI-ESP European American populationEA<br>
MAF","Clinical significance of variant from dbSNPClinical<br>
significance","Somatic status of existing variantSomatic<br>
status","Pubmed ID(s) of publications that cite existing<br>
variantPubmed","The source and identifier of a transcription factor<br>
binding profile (TFBP) aligned at this positionMotif name","The<br>
relative position of the variation in the aligned TFBPMotif<br>
position","A flag indicating if the variant falls in a high<br>
information position of the TFBPHigh info position","The difference in<br>
motif score of the reference and variant sequences for the TFBPMotif<br>
score change"<br>
".","19:5831713","C","ENSG00000156413","ENST00000528505","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","764","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","4","-","ENSP00000433811","-","-","-","-","-","-","-","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
".","19:5831713","C","ENSG00000156413","ENST00000526499","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","3059","-1","FUT6","HGNC","HGNC:4017","retained_intron","-","5","-","-","-","-","-","-","-","-","-","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
".","19:5831713","C","ENSG00000156413","ENST00000286955","Transcript","synonymous_variant","1908","855","285","P","CCA/CCG","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","-","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","1","CCDS12152.1","ENSP00000286955","-","-","2/2","-","Pfam_domain:PF00852","ENST00000286955.5:c.855A>G","ENST00000286955.5:c.855A>G(p.=)","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
".","19:5831713","C","ENSG00000156413","ENST00000531199","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","655","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","5","-","ENSP00000436413","-","-","-","-","-","-","-","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
".","19:5831713","C","ENSG00000156413","ENST00000532464","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","721","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","4","-","ENSP00000431880","-","-","-","-","-","-","-","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
".","19:5831713","C","ENSG00000156413","ENST00000529165","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","444","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","2","-","ENSP00000436547","-","-","-","-","-","-","-","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
".","19:5831713","C","ENSG00000156413","ENST00000527106","Transcript","synonymous_variant","1124","855","285","P","CCA/CCG","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","-","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","1","CCDS12152.1","ENSP00000432954","-","-","4/4","-","Pfam_domain:PF00852","ENST00000527106.3:c.855A>G","ENST00000527106.3:c.855A>G(p.=)","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
".","19:5831713","C","ENSG00000156413","ENST00000318336","Transcript","synonymous_variant","2050","855","285","P","CCA/CCG","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","-","-1","FUT6","HGNC","HGNC:4017","protein_coding","YES","2","CCDS12152.1","ENSP00000313398","-","-","3/3","-","Pfam_domain:PF00852","ENST00000318336.6:c.855A>G","ENST00000318336.6:c.855A>G(p.=)","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
".","19:5831713","C","ENSG00000171119","ENST00000303212","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","3389","1","NRTN","HGNC","HGNC:8007","protein_coding","YES","1","CCDS12151.1","ENSP00000302648","-","-","-","-","-","-","-","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
".","19:5831713","C","ENSG00000156413","ENST00000524754","Transcript","synonymous_variant","1495","855","285","P","CCA/CCG","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","-","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","1","CCDS12152.1","ENSP00000431708","-","-","3/3","-","Pfam_domain:PF00852","ENST00000524754.1:c.855A>G","ENST00000524754.1:c.855A>G(p.=)","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
".","19:5831713","C","ENSG00000156413","ENST00000531085","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","648","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","5","-","ENSP00000432161","-","-","-","-","-","-","-","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
".","19:5831713","C","ENSG00000156413","ENST00000592563","Transcript","<br>
synonymous_variant","855","855","285","P","CCA/CCG","rs13346240,<br>
rs112313064, COSM3766452,<br>
COSM3766451","-","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","1","-","ENSP00000466016","-","-","1/2","-","Pfam_domain:PF00852","ENST00000592563.1:c.855A>G","ENST00000592563.1:c.855A>G(p.=)","T:0.4357","C:0.02,<br>
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,<br>
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"<br>
<br>
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</blockquote></div><br></div>