This reports the protocol used to align the RiceAustraliensis_BACend_OA_CB_OMAP-20070815 features to indica-genome.
Tue Aug 21 14:12:44 2007


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

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

135769 RiceAustraliensis_BACend_OA_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 : 136871
# unique Features these alignments represent: 105024
% of total features these alignments represent : 77.35 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 13634
150	 12244
200	 14203
250	 10858
300	 10439
350	 10394
400	 10541
450	 11777
500	 11216
550	 10502
600	 8152
650	 5942
700	 3707
750	 1997
800	 876
10000	 389

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 116292
2000	 784
3000	 479
4000	 302
5000	 240
6000	 226
7000	 164
8000	 429
9000	 219
10000	 237
20000	 1181

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 85832
2	 12962
3	 3580
4	 1192
5	 652
6	 320
8	 281
9	 55
10	 54
20	 92
30	 4
40	 0
50	 0
100	 0

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 1
30	 29
40	 215
50	 836
60	 2554
70	 11988
80	 25569
90	 47111
100	 48568

Following is the final summary
# alignments : 136871
# unique Features these alignments represent: 105024
% of total features these alignments represent : 77.35 %
  

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