This reports the protocol used to align the RiceJaponica_BACend_OMAP features to tigrv4-genome. Fri Apr 14 18:41:55 2006 Source of RiceJaponica_BACend_OMAP : from Gramene markers database, originally Downloaded from genbank using the query '(CUGI Rice BAC end) AND (oryza [ORGN])' and only high quality sequence is extracted based on the information from genbank records Alignment procedure details --------------------------- 249729 RiceJaponica_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 : 368234 # unique Features these alignments represent: 237528 % of total features these alignments represent : 95.11 % Following is the GAP distribution Gaps # alignments -------- -------- 0 149271 1 35331 2 18811 3 11414 4 8743 5 7018 6 6972 7 6063 8 5766 9 4979 10 4788 20 26737 30 11710 40 7412 50 4913 60 3411 70 2454 80 1984 90 1628 100 1571 200 6370 300 3433 400 3215 500 2223 600 1419 700 1098 800 1065 900 913 10000 13661 Features with gaps > 40 bp are deleted # remaining Alignments : 305015 # unique Features these remaining alignments represent: 195755 % of total features these alignments represent : 78.39 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 12 19 260 29 4500 39 8513 49 13671 59 22133 69 34065 79 37322 89 43468 90 4965 91 5882 92 6879 93 7315 94 9018 95 7488 96 6847 97 7220 98 9960 99 16734 100 58763 Features less than 90 % coverage are deleted. # remaining Alignments : 136211 # unique Features these remaining alignments represent: 96302 % of total features these alignments represent : 38.56 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 67 91 100 92 131 93 266 94 567 95 1261 96 3073 97 8067 98 22494 99 55547 100 44638 Features less than 92 % identity are deleted. # remaining Alignments : 136044 # unique Features these remaining alignments represent: 96185 % of total features these alignments represent : 38.52 % Frequency distribution of the remaining features # hits # features -------- -------- 1 90100 2 2249 3 998 4 587 5 720 6 276 8 401 9 80 10 109 20 313 30 101 40 75 50 46 100 75 Features that hit more than thrice are deleted. # remaining Alignments : 97592 # unique Features these remaining alignments represent: 93347 % of total features these alignments represent : 37.38 %