This reports the protocol used to align the RiceGlaberrima_BACend_OMAP features to tigrv4-genome. Fri Apr 14 12:17:23 2006 Source of RiceGlaberrima_BACend_OMAP : from Gramene markers database, originally Downloaded from genbank nucleotide databse with keyword 'OG_BBa' Alignment procedure details --------------------------- 67158 RiceGlaberrima_BACend_OMAP are aligned to tigrv4-genome using blat with blat parameters -minScore=160 followed by PslReps with -minAli=0.90 -nearTop=0.01 -singleHit. This was followed by a filtering procedure described below and applied in general to 'Same Species Genomic' data sets. Initial summary # alignments : 97161 # unique Features these alignments represent: 62944 % of total features these alignments represent : 93.73 % Following is the GAP distribution Gaps # alignments -------- -------- 0 52347 1 11019 2 5052 3 3351 4 2242 5 1766 6 1540 7 1204 8 901 9 1005 10 743 20 3895 30 1907 40 1012 50 639 60 419 70 301 80 283 90 175 100 190 200 998 300 688 400 505 500 391 600 88 700 61 800 71 900 48 10000 1190 Features with gaps > 40 bp are deleted # remaining Alignments : 87984 # unique Features these remaining alignments represent: 57118 % of total features these alignments represent : 85.05 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 0 19 0 29 73 39 197 49 306 59 518 69 577 79 769 89 2154 90 600 91 892 92 1121 93 1522 94 2523 95 3984 96 6422 97 9763 98 14156 99 18877 100 23530 Features less than 90 % coverage are deleted. # remaining Alignments : 82804 # unique Features these remaining alignments represent: 53070 % of total features these alignments represent : 79.02 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 139 91 223 92 406 93 983 94 1881 95 3902 96 7295 97 13459 98 20827 99 28839 100 4850 Features less than 92 % identity are deleted. # remaining Alignments : 82442 # unique Features these remaining alignments represent: 52847 % of total features these alignments represent : 78.69 % Frequency distribution of the remaining features # hits # features -------- -------- 1 46322 2 2053 3 1181 4 858 5 595 6 354 8 865 9 97 10 104 20 268 30 45 40 29 50 15 100 50 Features that hit more than thrice are deleted. # remaining Alignments : 53971 # unique Features these remaining alignments represent: 49556 % of total features these alignments represent : 73.79 %