This reports the protocol used to align the RiceBrachyantha_BACend_OB__B_OMAP-20070815 features to indica-genome.
Tue Aug 21 12:20:42 2007


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

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

67364 RiceBrachyantha_BACend_OB__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 : 58572
# unique Features these alignments represent: 50026
% of total features these alignments represent : 74.26 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 8792
150	 6097
200	 4874
250	 4616
300	 4657
350	 4096
400	 4250
450	 4112
500	 3960
550	 3711
600	 3272
650	 2689
700	 1786
750	 1026
800	 469
10000	 165

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 53303
2000	 218
3000	 137
4000	 89
5000	 162
6000	 42
7000	 58
8000	 32
9000	 38
10000	 57
20000	 299

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 44876
2	 3538
3	 866
4	 292
5	 246
6	 98
8	 70
9	 9
10	 13
20	 12
30	 6
40	 0
50	 0
100	 0

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 3
40	 15
50	 86
60	 324
70	 944
80	 3167
90	 22787
100	 31246

Following is the final summary
# alignments : 58572
# unique Features these alignments represent: 50026
% of total features these alignments represent : 74.26 %
  

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