This reports the protocol used to align the Rice_ArrayConsensus_Affy57K features to tigrv4-genome. Fri Apr 14 17:01:35 2006 Source of Rice_ArrayConsensus_Affy57K : Downloaded from Affymetrix website Alignment procedure details --------------------------- 57194 Rice_ArrayConsensus_Affy57K are aligned to tigrv4-genome using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'Coding-SameSpecies' data sets. Initial summary # alignments : 57346 # unique Features these alignments represent: 55301 % of total features these alignments represent : 96.69 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 8 19 27 29 24 39 24 49 59 59 192 69 184 79 318 89 649 90 126 91 209 92 276 93 313 94 442 95 500 96 733 97 1180 98 2043 99 4941 100 45096 Alignments less than 95 % coverage are deleted # remaining Alignments : 54000 # unique Features these remaining alignments represent: 52268 % of total features these alignments represent : 91.39 % GAP distribution of the remaining features Gaps # alignments -------- -------- 1000 30412 2000 9870 3000 5995 4000 3216 5000 1694 6000 992 7000 615 8000 361 9000 236 10000 149 20000 375 Alignments with gaps > 4000 bp are deleted # remaining Alignments : 49493 # unique Features these remaining alignments represent: 47815 % of total features these alignments represent : 83.60 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 0 94 0 95 8 96 39 97 83 98 273 99 10337 100 38753 Frequency distribution of the remaining features # hits # features -------- -------- 1 47124 2 402 3 116 4 71 5 36 6 22 8 24 9 2 10 3 20 8 30 1 40 2 50 4 100 0 Features that hit more than four times are deleted. # remaining Alignments : 48560 # unique Features these remaining alignments represent: 47713 % of total features these alignments represent : 83.42 %