This reports the protocol used to align the RiceAlta_BACend_OA_BB_OMAP-20070815 features to indica-genome.
Tue Aug 21 12:05:28 2007


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

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

128732 RiceAlta_BACend_OA_BB_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 : 131694
# unique Features these alignments represent: 108075
% of total features these alignments represent : 83.95 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 13814
150	 14608
200	 10815
250	 10602
300	 10346
350	 10332
400	 10455
450	 9913
500	 9261
550	 8469
600	 7252
650	 6270
700	 4723
750	 2885
800	 1439
10000	 510

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 117830
2000	 868
3000	 443
4000	 322
5000	 245
6000	 261
7000	 140
8000	 124
9000	 131
10000	 91
20000	 973

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 93830
2	 9808
3	 2463
4	 881
5	 427
6	 257
8	 237
9	 60
10	 45
20	 64
30	 3
40	 0
50	 0
100	 0

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 14
40	 80
50	 318
60	 969
70	 6469
80	 13372
90	 40449
100	 70023

Following is the final summary
# alignments : 131694
# unique Features these alignments represent: 108075
% of total features these alignments represent : 83.95 %
  

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