This reports the protocol used to align the RiceRufipogon_BACend_OR_CB_OMAP-20070815 features to indica-genome.
Tue Aug 21 13:22:20 2007


Source of RiceRufipogon_BACend_OR_CB_OMAP-20070815 : from Gramene markers database, originally Downloaded from genbank nucleotide databse with keyword 'OR_CBa'   

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

70982 RiceRufipogon_BACend_OR_CB_OMAP-20070815 are aligned to indica-genome using blat with blat parameters -minIdentity=50 -minScore=10 -maxGap=3 followed by PslReps with -minNearTopSize=75 -minAli=0.25. This was followed by a filtering procedure described below and applied in general to 'OMAPSpecies-Genomic' data sets.

Initial summary
# alignments : 101015
# unique Features these alignments represent: 70547
% of total features these alignments represent : 99.39 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 234
150	 586
200	 710
250	 840
300	 951
350	 976
400	 1541
450	 2062
500	 2667
550	 4045
600	 7286
650	 12153
700	 17651
750	 19914
800	 16188
10000	 13211

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 93687
2000	 531
3000	 376
4000	 271
5000	 240
6000	 125
7000	 102
8000	 106
9000	 111
10000	 95
20000	 461

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 60064
2	 4666
3	 1961
4	 1189
5	 853
6	 514
8	 630
9	 168
10	 135
20	 313
30	 26
40	 12
50	 12
100	 4

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 2
60	 16
70	 42
80	 134
90	 1493
100	 99328

Following is the final summary
# alignments : 101015
# unique Features these alignments represent: 70547
% of total features these alignments represent : 99.39 %
  

Last modified: Thu Sep 13 15:01:03 2007