This reports the protocol used to align the Ryegrass_MethylFilterCluster_Orion features to tigrv4-genome.
Mon Apr 24 16:39:36 2006


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

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

80162 Ryegrass_MethylFilterCluster_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 : 24206
# unique Features these alignments represent: 22490
% of total features these alignments represent : 28.06 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 5750
150	 3063
200	 2873
250	 2532
300	 2063
350	 1636
400	 1347
450	 1143
500	 858
550	 664
600	 535
650	 397
700	 302
750	 225
800	 179
10000	 639

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 18534
# unique Features these remaining alignments represent: 17663
% of total features these alignments represent : 22.03 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 17207
2000	 346
3000	 66
4000	 48
5000	 29
6000	 26
7000	 40
8000	 20
9000	 33
10000	 23
20000	 166

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 17667
# unique Features these remaining alignments represent: 16898
% of total features these alignments represent : 21.08 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 16436
2	 337
3	 70
4	 20
5	 17
6	 7
8	 8
9	 0
10	 1
20	 1
30	 0
40	 0
50	 0
100	 1

 Features that hit more than thrice are deleted. 
# remaining Alignments : 17320
# unique Features these remaining alignments represent: 16843
% of total features these alignments represent : 21.01 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 2
30	 27
40	 98
50	 205
60	 323
70	 587
80	 1952
90	 9933
100	 4193

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 16707
# unique Features these remaining alignments represent: 16289
% of total features these alignments represent : 20.32 %

Following is the final summary
# alignments : 16707
# unique Features these alignments represent: 16289
% of total features these alignments represent : 20.32 %