| panzea_SNPs_20160417.zip | These are legacy SNPs from the previous version panzea web site. There are 4 files in this directory:
SNPpos_agpv2.bed: SNP positions in B73 agpv2 coordinates.
SNPpos_agpv3.bed: SNP positions in B73 agpv3 coordinates.
context_full.fasta: Context sequence of the SNPs. One sequence for each SNP.
context_left_right.fasta: Context sequence of the SNPs. Two flanking sequences for each SNP. Both sequences are in the same orientation as the sequences in the file context_full.fasta.
Note:
The BED file format is as described in https://genome.ucsc.edu/FAQ/FAQformat.html#format1 . You can open this file in Excel. The columns are:
1) chromosome name;
2) start position (0-based, the first nucleotide of the chromsome is position 0);
3) end position (1-based, the first nucleotide of the chromsome is position 1);
4) SNP name;
5) score. This value is the percentage of identical nucleotides in the alignment between context and reference times 1000 ;
6) strand. The relative strand of the context vs the reference genome
Some of SNPs with context sequences, but not in the bed files. This is because we cannot identify a postion based on the alignment between context sequence and the reference genome.
| agpv2 and agpv3 | | bed and fasta | 4/17/2016 | 1.15mb |