This reports the protocol used to align the Ryegrass_MethylFilterCluster_Orion features to Maize_BACs_20060126.
Mon Feb 13 18:44:34 2006


Source of Ryegrass_MethylFilterCluster_Orion : Obtained from Orion Genomics 

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

191338 Ryegrass_MethylFilterCluster_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 : 18045
# unique Features these alignments represent: 10371
% of total features these alignments represent : 5.42 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 7950
150	 1844
200	 1485
250	 1065
300	 974
350	 861
400	 792
450	 604
500	 591
550	 460
600	 494
650	 333
700	 223
750	 163
800	 127
10000	 79

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 10133
# unique Features these remaining alignments represent: 6352
% of total features these alignments represent : 3.32 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 9901
2000	 43
3000	 5
4000	 6
5000	 1
6000	 12
7000	 4
8000	 4
9000	 8
10000	 4
20000	 29

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 9955
# unique Features these remaining alignments represent: 6229
% of total features these alignments represent : 3.26 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 4783
2	 675
3	 223
4	 119
5	 174
6	 105
8	 127
9	 6
10	 6
20	 11
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 6802
# unique Features these remaining alignments represent: 5681
% of total features these alignments represent : 2.97 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 3
30	 53
40	 134
50	 372
60	 965
70	 1049
80	 1120
90	 1832
100	 1274

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 5391
# unique Features these remaining alignments represent: 4518
% of total features these alignments represent : 2.36 %

Following is the final summary
# alignments : 5391
# unique Features these alignments represent: 4518
% of total features these alignments represent : 2.36 %