This reports the protocol used to align the RiceGranulata_BACend_OG_AB_OMAP-20070815 features to indica-genome.
Tue Aug 21 13:52:46 2007


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

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

138171 RiceGranulata_BACend_OG_AB_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 : 102039
# unique Features these alignments represent: 84170
% of total features these alignments represent : 60.92 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 20479
150	 12127
200	 8923
250	 7737
300	 7721
350	 7680
400	 6705
450	 5949
500	 5578
550	 5036
600	 4455
650	 3822
700	 2657
750	 1769
800	 870
10000	 531

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 92379
2000	 438
3000	 203
4000	 281
5000	 211
6000	 146
7000	 85
8000	 82
9000	 64
10000	 68
20000	 473

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 72637
2	 8338
3	 1830
4	 641
5	 363
6	 156
8	 124
9	 31
10	 10
20	 36
30	 1
40	 2
50	 1
100	 0

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 4
30	 41
40	 202
50	 1093
60	 3447
70	 9526
80	 14848
90	 32995
100	 39883

Following is the final summary
# alignments : 102039
# unique Features these alignments represent: 84170
% of total features these alignments represent : 60.92 %
  

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