This reports the protocol used to align the RiceAustraliensis_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 17:54:48 2006


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

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

128599 RiceAustraliensis_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 : 167386
# unique Features these alignments represent: 106887
% of total features these alignments represent : 83.12 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 12077
150	 11671
200	 13174
250	 10224
300	 9778
350	 9370
400	 9931
450	 11166
500	 13031
550	 13342
600	 12568
650	 11684
700	 10161
750	 8839
800	 6391
10000	 3979

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 155545
# unique Features these remaining alignments represent: 97697
% of total features these alignments represent : 75.97 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 129034
2000	 547
3000	 200
4000	 217
5000	 156
6000	 190
7000	 344
8000	 184
9000	 191
10000	 148
20000	 963

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 129998
# unique Features these remaining alignments represent: 81733
% of total features these alignments represent : 63.56 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 65357
2	 8524
3	 2753
4	 1506
5	 823
6	 530
8	 1240
9	 176
10	 158
20	 474
30	 78
40	 69
50	 26
100	 18

 Features that hit more than thrice are deleted. 
# remaining Alignments : 90664
# unique Features these remaining alignments represent: 76634
% of total features these alignments represent : 59.59 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 5
30	 34
40	 223
50	 717
60	 2653
70	 10427
80	 15781
90	 23769
100	 37055

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 87471
# unique Features these remaining alignments represent: 73872
% of total features these alignments represent : 57.44 %

Following is the final summary
# alignments : 87471
# unique Features these alignments represent: 73872
% of total features these alignments represent : 57.44 %