This reports the protocol used to align the Rice_CDS features to tigrv4-genome. Fri Apr 14 17:52:03 2006 Source of Rice_CDS : from Gramene markers database, originally Downloaded from Genbank with query '(txid4530[ORGN] AND complete[TITL] AND cds[TITL]) NOT (Mitochondrion[ALL] OR Chloroplast[ALL] OR Mitochondrial[ALL]) )' Alignment procedure details --------------------------- 72229 Rice_CDS 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 : 76881 # unique Features these alignments represent: 70728 % of total features these alignments represent : 97.92 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 16 19 63 29 33 39 60 49 55 59 251 69 229 79 276 89 405 90 52 91 66 92 102 93 105 94 126 95 210 96 384 97 376 98 599 99 1177 100 72257 Alignments less than 95 % coverage are deleted # remaining Alignments : 74836 # unique Features these remaining alignments represent: 69212 % of total features these alignments represent : 95.82 % GAP distribution of the remaining features Gaps # alignments -------- -------- 1000 41980 2000 13800 3000 8802 4000 4476 5000 2220 6000 1255 7000 756 8000 425 9000 314 10000 183 20000 446 Alignments with gaps > 4000 bp are deleted # remaining Alignments : 69058 # unique Features these remaining alignments represent: 63619 % of total features these alignments represent : 88.08 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 1 92 0 93 0 94 0 95 3 96 8 97 39 98 237 99 18110 100 50660 Frequency distribution of the remaining features # hits # features -------- -------- 1 62370 2 631 3 182 4 110 5 62 6 62 8 38 9 15 10 12 20 88 30 23 40 13 50 5 100 7 Features that hit more than four times are deleted. # remaining Alignments : 64618 # unique Features these remaining alignments represent: 63293 % of total features these alignments represent : 87.63 %