This reports the protocol used to align the Maize_WGS_JGI features to Maize_BACs_20060126. Sat Feb 18 14:16:59 2006 Source of Maize_WGS_JGI : These are Maize WGS reads from Joint Genome Institute obtained by Bonnie Alignment procedure details --------------------------- 1124441 Maize_WGS_JGI are aligned to Maize_BACs_20060126 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 # aligments : 1868880 # unique Features these alignments represent: 833189 % of total features these alignments represent : 74.10 % Following is the Gap distribution Gaps # alignments -------- -------- 0 114537 1 130164 2 127578 3 107577 4 84617 5 68829 6 58463 7 51786 8 46786 9 42439 10 38325 20 240949 30 116422 40 62394 50 39150 60 28651 70 22046 80 15250 90 12306 100 9395 200 56766 300 22434 400 11616 500 7815 600 4359 700 3436 800 2762 900 2654 10000 87023 Features with gaps > 40 bp are deleted # remaining Aligments : 1290866 # unique Features these represent alignments represent: 562029 % of total features these alignments represent : 49.98 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 0 19 8220 29 46428 39 31528 49 31290 59 32536 69 35340 79 47181 89 197298 90 63999 91 79345 92 97686 93 111683 94 121593 95 121534 96 108400 97 87847 98 51519 99 15285 100 2154 Features less than 90 % coverage are deleted. # remaining Aligments : 797783 # unique Features these represent alignments represent: 292734 % of total features these alignments represent : 26.03 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 483 91 2949 92 11465 93 29329 94 64467 95 114114 96 159095 97 171835 98 155266 99 85780 100 3000 Features less than 92 % identity are deleted. # remaining Aligments : 794351 # unique Features these represent alignments represent: 290764 % of total features these alignments represent : 25.86 % Frequency distribution of the remaining features # hits # features -------- -------- 1 129306 2 59998 3 32951 4 21096 5 15586 6 8813 8 10933 9 2968 10 2196 20 6212 30 614 40 80 50 10 100 1 Features that hit more than thrice are deleted. # remaining Aligments : 348155 # unique Features these represent alignments represent: 222255 % of total features these alignments represent : 19.77 %