This reports the protocol used to align the Maize_WGS_JGI features to tigrv4-genome. Mon Apr 17 15:39:45 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 tigrv4-genome using blat with blat parameters -minIdentity=50 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'CrossSpecies-Genomic' data sets. Initial summary # aligments : 565382 # unique Features these alignments represent: 365586 % of total features these alignments represent : 32.51 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 156185 150 44600 200 32375 250 27551 300 25100 350 23473 400 23291 450 23033 500 21666 550 19772 600 19687 650 17012 700 12218 750 9572 800 10671 10000 99176 Alignments with matches less than 100 bp are filtered # remaining Aligments : 410119 # unique Features these represent alignments represent: 248728 % of total features these alignments represent : 22.12 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 380501 2000 501 3000 375 4000 385 5000 486 6000 209 7000 213 8000 308 9000 598 10000 77 20000 933 Alignments with gaps > 4000 bp are filtered # remaining Aligments : 381762 # unique Features these represent alignments represent: 228793 % of total features these alignments represent : 20.35 % Frequency distribution of the remaining features # hits # features -------- -------- 1 169704 2 25268 3 9062 4 9313 5 7162 6 4402 8 2215 9 554 10 490 20 574 30 32 40 7 50 4 100 6 Features that hit more than thrice are deleted. # remaining Aligments : 247426 # unique Features these represent alignments represent: 204034 % of total features these alignments represent : 18.15 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 1 20 182 30 2374 40 11476 50 20227 60 28979 70 69225 80 34199 90 35623 100 45140 Alignments with percent identity lower than 60 deleted. # remaining Aligments : 188050 # unique Features these represent alignments represent: 153293 % of total features these alignments represent : 13.63 % Following is the final summary # alignments : 17152 # unique Features these alignments represent: 13991 % of total features these alignments represent : 13.99 %