################################################################### # Data release of 80 Arabidopsis thaliana accessions. # date: 2010_05_12 ################################################################### Data analysis description: The genomes have been analyzed both separately and in a joint approach. This file describes the content of TAIR8.genome_matrix_2010_05_12.txt TAIR9.genome_matrix_2010_03_25.txt These files describe the position-wise base call of 80 accessions. As the short read analysis was performed against the TAIR8 assembly we afterwards mapped the TAIR8 positions to their respective TAIR9 positions. Thus, a minor fraction of TAIR9 assembly positions do NOT feature base calls (i.e. the additional ones introduced into the assembly when upgrading from TAIR8 to TAIR9). There are 9 different base call annotations: A/C/G/T = base call of the respective nucleotide - = deletion (predicted based on gapped short read alignments) D = deletion (predicted based on stretched read mates (SV call)) Z = zero coverage (but no SV deletion predicted) N = No call possible (but neither D nor Z applicable) R = repetitive position (no call in focal genome and highly repetitive in Col-0) ################################################################### # File format ################################################################### The format of TAIR8.genome_matrix_2010_05_12.txt and TAIR9.genome_matrix_2010_03_25.txt is identical. Each of them features 83 columns: Followed by the calls of the 80 accessions: Agu1 Bak-2 Bak-7 Cdm-0 Del-10 Dog-4 Don-0 Ey1.5-2 Fei-0 HKT2-4 ice102 ice104 ice106 ice107 ice111 ice112 ice119 ice120 ice127 ice130 ice134 ice138 ice150 ice152 ice153 ice163 ice169 ice173 ice181 ice1 ice212 ice213 ice216 ice21 ice226 ice228 ice29 ice33 ice36 ice49 ice50 ice60 ice61 ice63 ice70 ice71 ice72 ice73 ice75 ice79 ice7 ice91 ice92 ice93 ice97 ice98 Istisu-1 Kastel-1 Koch-1 Lag2-2 Leo-1 Lerik1-3 Nemrut-1 Mer-6 Nie1-2 Ped-0 Pra-6 Qui-0 Rü3.1-31 Sha Star-8 Tü-SB30-3 Tü-Scha-9 Tü-V-13 Tü-Wa1-2 Vash-1 Vie-0 Wal-HäsB-4 Xan-1 Yeg-1 ------------------------------------------------------------------- Tuebingen, Germany, 2010 Questions? korbinian.schneeberger@tuebingen.mpg.de