MHC_454

This compressed file contains two folders with all of the raw 454 files for MHCIIb for this project. Each file name includes on of three libraries (02, 03, or 04) and a MID number 1-153. These numbers correspond to various spreadsheets in the R scripts folder

Genotypes_Phenotypes_Expression_data

Genotypes_Phenotypes_Expression_dat

DATA2

Genotypes of both the anadromous parents and the precocious parr identified by Colony. Genotypes of precocious parr have been inferred by Colony

DATA1

Genotypes of the fish sampled: ID(A:fry ; P:anadromous)type(fry/anadromous); sex of the anadromous fish; father and mother assigned to each fry. " * " corresponds to precocious parr

Distribution of SNPs on the basis of their location in respective predicted gene models in soybean genome.

<p>SNPs were categorised using gene structure information retrieved from phytozome (<a href="http://www.phytozome.org" target="_blank">www.phytozome.org</a>).</p

Phylogenetic tree showing genetic distance among a set of eight diverse soybean cultivars.

<p>The phylogenetic tree was constructed on the basis of 10,120 SNPs identified using the GBS approach.</p

Sequence coverage and SNP distribution.

<p>(a) Distribution of mapped sequence reads (scaled down to 1/10) and SNPs identified using a GBS approach, and (b) corresponding frequency of genes and transposons identified in the same bins on soybean chromosome 5. All the transposons and genes were retrieved from the soybase and phytozome database respectively (<a href="http://www.soybase.org" target="_blank">www.soybase.org</a>, <a href="http://www.phytozome.org" target="_blank">www.phytozome.org</a>).</p

Impact of selective amplification on the number and depth of coverage of SNPs.

<p>(a) Schematic representation of an <i>Ape</i>KI restriction fragment flanked by suitable ligated adapters and the position of standard or selective primers, (b) Comparison of the number of SNPs and sequence read depth obtained with different sets of primers, and (c) number of SNPs and mean depth of coverage observed with selective amplification of <i>Ape</i>KI digested fragments with AC selective primers at different levels of multiplexing.</p

Summary of sequenced raw and processed reads in eight soybean genotypes obtained on an Illumina Genome Analyzer II.

<p>Summary of sequenced raw and processed reads in eight soybean genotypes obtained on an Illumina Genome Analyzer II.</p

<i>In silico</i> analysis of restriction enzyme sites in the soybean genome.

<p>Fragment size distribution obtained by <i>in silico</i> digestion of soybean chromosome 5 with <i>Ape</i>K1, <i>Pst</i>1 and <i>Mse</i>1 restriction enzymes showing a higher percentage of <i>Ape</i>K1 fragments in a suitable range for genotyping by sequencing.</p