This reports the protocol used to align the RiceNivara_BACend_OR_BB_OMAP-20070815 features to indica-genome.
Tue Aug 21 14:27:24 2007


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

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

106124 RiceNivara_BACend_OR_BB_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 : 153241
# unique Features these alignments represent: 104703
% of total features these alignments represent : 98.66 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 443
150	 889
200	 1384
250	 1698
300	 2291
350	 2417
400	 3787
450	 5424
500	 8059
550	 10973
600	 16399
650	 21609
700	 25790
750	 23970
800	 16503
10000	 11605

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 142324
2000	 836
3000	 569
4000	 329
5000	 340
6000	 215
7000	 147
8000	 162
9000	 190
10000	 95
20000	 629

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 87805
2	 7419
3	 3186
4	 1893
5	 1424
6	 842
8	 1049
9	 330
10	 202
20	 485
30	 47
40	 7
50	 9
100	 5

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 0
40	 1
50	 6
60	 16
70	 70
80	 239
90	 2549
100	 150360

Following is the final summary
# alignments : 153241
# unique Features these alignments represent: 104703
% of total features these alignments represent : 98.66 %
  

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