This reports the protocol used to align the RiceMinuta_BACend_OM__B_OMAP-20070815 features to indica-genome.
Tue Aug 21 14:17:15 2007


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

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

169460 RiceMinuta_BACend_OM__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 : 189959
# unique Features these alignments represent: 150039
% of total features these alignments represent : 88.54 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 10623
150	 11771
200	 13794
250	 14556
300	 15615
350	 16910
400	 17391
450	 17818
500	 18107
550	 17485
600	 15301
650	 10473
700	 6117
750	 2738
800	 958
10000	 302

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 167297
2000	 1155
3000	 873
4000	 601
5000	 441
6000	 381
7000	 254
8000	 216
9000	 199
10000	 195
20000	 1493

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 128729
2	 13535
3	 3791
4	 1505
5	 946
6	 581
8	 533
9	 148
10	 100
20	 165
30	 3
40	 3
50	 0
100	 0

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 8
40	 95
50	 309
60	 968
70	 4533
80	 18601
90	 71932
100	 93513

Following is the final summary
# alignments : 189959
# unique Features these alignments represent: 150039
% of total features these alignments represent : 88.54 %
  

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