This reports the protocol used to align the Ryegrass_MethylFilter_Orion features to Maize_BACs_20060126.
Mon Feb 13 18:51:11 2006


Source of Ryegrass_MethylFilter_Orion : Obtained from Orion Genomics 

Alignment procedure details 
--------------------------- 

398333 Ryegrass_MethylFilter_Orion are aligned to Maize_BACs_20060126 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
# alignments : 26533
# unique Features these alignments represent: 15502
% of total features these alignments represent : 3.89 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 12801
150	 2944
200	 2160
250	 1696
300	 1359
350	 1140
400	 996
450	 735
500	 660
550	 567
600	 550
650	 369
700	 235
750	 186
800	 114
10000	 21

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 13787
# unique Features these remaining alignments represent: 9095
% of total features these alignments represent : 2.28 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 13566
2000	 11
3000	 3
4000	 3
5000	 2
6000	 10
7000	 9
8000	 3
9000	 9
10000	 6
20000	 31

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 13583
# unique Features these remaining alignments represent: 8950
% of total features these alignments represent : 2.25 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 7128
2	 911
3	 263
4	 130
5	 185
6	 112
8	 195
9	 7
10	 6
20	 13
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 9739
# unique Features these remaining alignments represent: 8302
% of total features these alignments represent : 2.08 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 2
30	 65
40	 142
50	 436
60	 1116
70	 1239
80	 1495
90	 3071
100	 2173

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 8109
# unique Features these remaining alignments represent: 6962
% of total features these alignments represent : 1.75 %

Following is the final summary
# alignments : 8109
# unique Features these alignments represent: 6962
% of total features these alignments represent : 1.75 %