This reports the protocol used to align the Maize_MAGI_ISU features to tigrv4-genome. Fri Apr 14 18:32:32 2006 Source of Maize_MAGI_ISU : Maize_ISU_MAGIs_3_1_w_singleton : from Gramene markers database, originally Downloaded from http://magi.plantgenomics.iastate.edu/downloadall.html Alignment procedure details --------------------------- 192954 Maize_MAGI_ISU 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 : 69237 # unique Features these alignments represent: 48758 % of total features these alignments represent : 25.27 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 20945 150 8863 200 7329 250 5872 300 4537 350 3801 400 3023 450 2487 500 1928 550 1635 600 1355 650 1090 700 902 750 843 800 740 10000 3887 Alignments with matches less than 100 bp are filtered # remaining Alignments : 48527 # unique Features these remaining alignments represent: 37742 % of total features these alignments represent : 19.56 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 42911 2000 2701 3000 758 4000 296 5000 183 6000 86 7000 87 8000 69 9000 67 10000 42 20000 301 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 46666 # unique Features these remaining alignments represent: 36239 % of total features these alignments represent : 18.78 % Frequency distribution of the remaining features # hits # features -------- -------- 1 35420 2 679 3 78 4 31 5 12 6 2 8 7 9 3 10 0 20 6 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 37012 # unique Features these remaining alignments represent: 36177 % of total features these alignments represent : 18.75 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 3 30 32 40 155 50 362 60 636 70 1184 80 4345 90 23136 100 7159 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 35919 # unique Features these remaining alignments represent: 35169 % of total features these alignments represent : 18.23 % Following is the final summary # alignments : 35919 # unique Features these alignments represent: 35169 % of total features these alignments represent : 18.23 %