This reports the protocol used to align the RiceIndica_ESTcluster_BGI features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 18:46:40 2007


Source of RiceIndica_ESTcluster_BGI : Oryza indica clusters downloaded from http://btn.genomics.org.cn/ 

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

23559 RiceIndica_ESTcluster_BGI are aligned to Oryza_sativa_indica-chromosome-20070724 using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'Coding-SameSpecies' data sets.

Initial summary
# alignments : 23012
# unique Features these alignments represent: 22060
% of total features these alignments represent : 93.64 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 0
19	 2
29	 5
39	 23
49	 51
59	 138
69	 204
79	 254
89	 469
90	 75
91	 77
92	 122
93	 134
94	 178
95	 201
96	 314
97	 505
98	 957
99	 2368
100	 16935

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 21082
# unique Features these remaining alignments represent: 20223
% of total features these alignments represent : 85.84 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 15910
2000	 3000
3000	 1210
4000	 442
5000	 179
6000	 101
7000	 46
8000	 28
9000	 13
10000	 12
20000	 63

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 20562
# unique Features these remaining alignments represent: 19717
% of total features these alignments represent : 83.69 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 5
95	 41
96	 94
97	 300
98	 1280
99	 8815
100	 10027

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 19278
2	 405
3	 22
4	 5
5	 1
6	 1
8	 1
9	 0
10	 0
20	 2
30	 1
40	 0
50	 0
100	 0

 Features that hit more than four times are deleted.  
# remaining Alignments : 20174
# unique Features these remaining alignments represent: 19710
% of total features these alignments represent : 83.66 %
  

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