This reports the protocol used to align the RiceOfficinalis_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 17:04:14 2006


Source of RiceOfficinalis_BACend_OMAP : from Gramene markers database, type GSS, species Oryza officinalis 

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

103251 RiceOfficinalis_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 : 144338
# unique Features these alignments represent: 94825
% of total features these alignments represent : 91.84 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 5372
150	 5367
200	 6479
250	 6522
300	 6943
350	 7098
400	 7712
450	 8379
500	 9164
550	 11554
600	 13636
650	 15998
700	 15176
750	 12461
800	 7505
10000	 4972

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 139079
# unique Features these remaining alignments represent: 90479
% of total features these alignments represent : 87.63 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 121397
2000	 1033
3000	 401
4000	 365
5000	 252
6000	 251
7000	 140
8000	 155
9000	 126
10000	 129
20000	 923

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 123196
# unique Features these remaining alignments represent: 79767
% of total features these alignments represent : 77.26 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 67025
2	 6853
3	 1665
4	 968
5	 625
6	 394
8	 857
9	 198
10	 190
20	 740
30	 177
40	 48
50	 14
100	 13

 Features that hit more than thrice are deleted. 
# remaining Alignments : 85726
# unique Features these remaining alignments represent: 75543
% of total features these alignments represent : 73.16 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 6
40	 58
50	 271
60	 713
70	 3119
80	 8553
90	 31618
100	 41388

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 84782
# unique Features these remaining alignments represent: 74707
% of total features these alignments represent : 72.35 %

Following is the final summary
# alignments : 84782
# unique Features these alignments represent: 74707
% of total features these alignments represent : 72.35 %