This reports the protocol used to align the Sorghum_MethylFilter_Orion features to tigrv4-genome. Fri Apr 14 17:26:10 2006 Source of Sorghum_MethylFilter_Orion : Sorghum_Orion_Genethresher_reads, from Gramene markers database, originally these are obtained from Orion Genomics. Alignment procedure details --------------------------- 136197 Sorghum_MethylFilter_Orion are aligned to tigrv4-genome using blat with blat parameters -minIdentity=50 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'CrossSpecies-Genomic' data sets. Initial summary # alignments : 67747 # unique Features these alignments represent: 57111 % of total features these alignments represent : 41.93 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 18946 150 10766 200 7122 250 5552 300 4381 350 3495 400 2961 450 2591 500 2030 550 1755 600 1461 650 1631 700 1495 750 1180 800 589 10000 1792 Alignments with matches less than 100 bp are filtered # remaining Alignments : 49074 # unique Features these remaining alignments represent: 41555 % of total features these alignments represent : 30.51 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 42790 2000 1508 3000 278 4000 173 5000 83 6000 54 7000 79 8000 61 9000 44 10000 42 20000 313 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 44749 # unique Features these remaining alignments represent: 38031 % of total features these alignments represent : 27.92 % Frequency distribution of the remaining features # hits # features -------- -------- 1 35316 2 1563 3 289 4 202 5 116 6 197 8 270 9 16 10 29 20 32 30 1 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 39309 # unique Features these remaining alignments represent: 37168 % of total features these alignments represent : 27.29 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 6 30 41 40 163 50 585 60 1348 70 2576 80 4543 90 21296 100 8751 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 37368 # unique Features these remaining alignments represent: 35501 % of total features these alignments represent : 26.07 % Following is the final summary # alignments : 37368 # unique Features these alignments represent: 35501 % of total features these alignments represent : 26.07 %