This reports the protocol used to align the Ryegrass_MethylFilter_Orion features to tigrv4-genome.
Fri Apr 14 18:13:28 2006


Source of Ryegrass_MethylFilter_Orion : from Gramene markers database, originally Obtained from Orion Genomics 

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

398333 Ryegrass_MethylFilter_Orion 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
# alignments : 81248
# unique Features these alignments represent: 66901
% of total features these alignments represent : 16.80 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 22533
150	 11739
200	 10216
250	 8512
300	 6656
350	 5176
400	 3956
450	 2993
500	 2265
550	 1742
600	 1583
650	 1357
700	 902
750	 809
800	 612
10000	 197

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 58992
# unique Features these remaining alignments represent: 48489
% of total features these alignments represent : 12.17 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 56854
2000	 125
3000	 65
4000	 71
5000	 78
6000	 63
7000	 62
8000	 39
9000	 60
10000	 46
20000	 329

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 57115
# unique Features these remaining alignments represent: 46945
% of total features these alignments represent : 11.79 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 43730
2	 1382
3	 289
4	 309
5	 328
6	 403
8	 402
9	 44
10	 18
20	 24
30	 7
40	 3
50	 2
100	 4

 Features that hit more than thrice are deleted. 
# remaining Alignments : 47361
# unique Features these remaining alignments represent: 45401
% of total features these alignments represent : 11.40 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 7
30	 117
40	 267
50	 571
60	 1728
70	 2489
80	 5435
90	 25227
100	 11520

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 44880
# unique Features these remaining alignments represent: 43264
% of total features these alignments represent : 10.86 %

Following is the final summary
# alignments : 44880
# unique Features these alignments represent: 43264
% of total features these alignments represent : 10.86 %