This reports the protocol used to align the RiceCoarctata_BACend_OC__B_OMAP-20070815 features to indica-genome.
Tue Aug 21 14:18:23 2007


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

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

195285 RiceCoarctata_BACend_OC__B_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 : 134968
# unique Features these alignments represent: 122018
% of total features these alignments represent : 62.48 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 19268
150	 9953
200	 9848
250	 9066
300	 9603
350	 9462
400	 9641
450	 9503
500	 10120
550	 9940
600	 9116
650	 7427
700	 5470
750	 3459
800	 1897
10000	 1195

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 129903
2000	 1037
3000	 352
4000	 269
5000	 342
6000	 156
7000	 114
8000	 113
9000	 49
10000	 99
20000	 527

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 114272
2	 5638
3	 1111
4	 338
5	 371
6	 156
8	 48
9	 10
10	 12
20	 39
30	 17
40	 2
50	 1
100	 3

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 2
30	 35
40	 134
50	 580
60	 2152
70	 4242
80	 8467
90	 36621
100	 82735

Following is the final summary
# alignments : 134968
# unique Features these alignments represent: 122018
% of total features these alignments represent : 62.48 %
  

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