This reports the protocol used to align the RiceGlaberrima_BACend_OG_BB_OMAP-20070815 features to indica-genome.
Tue Aug 21 13:15:35 2007


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

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

66821 RiceGlaberrima_BACend_OG_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 : 83854
# unique Features these alignments represent: 64998
% of total features these alignments represent : 97.27 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 886
150	 2365
200	 3089
250	 3482
300	 4032
350	 4291
400	 4861
450	 5075
500	 5868
550	 6568
600	 8439
650	 10009
700	 10346
750	 7895
800	 4393
10000	 2255

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 78743
2000	 443
3000	 266
4000	 199
5000	 197
6000	 107
7000	 105
8000	 65
9000	 58
10000	 43
20000	 391

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 56741
2	 4549
3	 1523
4	 696
5	 554
6	 322
8	 308
9	 93
10	 65
20	 134
30	 8
40	 1
50	 2
100	 2

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 1
40	 2
50	 5
60	 27
70	 78
80	 274
90	 2894
100	 80573

Following is the final summary
# alignments : 83854
# unique Features these alignments represent: 64998
% of total features these alignments represent : 97.27 %
  

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