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 %