This reports the protocol used to align the RiceAlta_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 17:03:02 2006


Source of RiceAlta_BACend_OMAP : from Gramene markers database, originally Downloaded from genbank nucleotide databse with keyword 'OA_BBa'   

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

128732 RiceAlta_BACend_OMAP 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 : 145760
# unique Features these alignments represent: 110521
% of total features these alignments represent : 85.85 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 14618
150	 16185
200	 12487
250	 12122
300	 11339
350	 10546
400	 10341
450	 11046
500	 9944
550	 9222
600	 8129
650	 7532
700	 5514
750	 3782
800	 2022
10000	 931

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 131415
# unique Features these remaining alignments represent: 98569
% of total features these alignments represent : 76.57 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 114685
2000	 900
3000	 386
4000	 316
5000	 185
6000	 154
7000	 139
8000	 128
9000	 115
10000	 76
20000	 778

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 116287
# unique Features these remaining alignments represent: 88290
% of total features these alignments represent : 68.58 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 77064
2	 6672
3	 1833
4	 861
5	 471
6	 290
8	 596
9	 119
10	 90
20	 214
30	 25
40	 19
50	 10
100	 26

 Features that hit more than thrice are deleted. 
# remaining Alignments : 95907
# unique Features these remaining alignments represent: 85569
% of total features these alignments represent : 66.47 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 14
40	 104
50	 281
60	 1007
70	 5677
80	 10219
90	 27055
100	 51550

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 94691
# unique Features these remaining alignments represent: 84494
% of total features these alignments represent : 65.64 %

Following is the final summary
# alignments : 94691
# unique Features these alignments represent: 84494
% of total features these alignments represent : 65.64 %