This reports the protocol used to align the RiceOfficinalis_BACend_OO__B_OMAP-20070815 features to indica-genome.
Tue Aug 21 12:54:33 2007


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

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

101091 RiceOfficinalis_BACend_OO__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 : 118553
# unique Features these alignments represent: 92465
% of total features these alignments represent : 91.47 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 4921
150	 5207
200	 5832
250	 6155
300	 6460
350	 6890
400	 7473
450	 7793
500	 8466
550	 9865
600	 10871
650	 11807
700	 10830
750	 8496
800	 4765
10000	 2722

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 103121
2000	 976
3000	 804
4000	 383
5000	 324
6000	 275
7000	 160
8000	 110
9000	 139
10000	 141
20000	 1155

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 79135
2	 8172
3	 2409
4	 990
5	 658
6	 405
8	 405
9	 106
10	 65
20	 117
30	 2
40	 1
50	 0
100	 0

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 17
40	 66
50	 236
60	 660
70	 3239
80	 11051
90	 46500
100	 56784

Following is the final summary
# alignments : 118553
# unique Features these alignments represent: 92465
% of total features these alignments represent : 91.47 %
  

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