This reports the protocol used to align the RiceIndica_EST_BGI features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 14:47:42 2007


Source of RiceIndica_EST_BGI : Oryza indica ESTs downloaded from http://btn.genomics.org.cn/ 

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

85719 RiceIndica_EST_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 : 93413
# unique Features these alignments represent: 79951
% of total features these alignments represent : 93.27 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 0
19	 0
29	 23
39	 126
49	 163
59	 400
69	 472
79	 794
89	 2689
90	 609
91	 714
92	 843
93	 1065
94	 1405
95	 2040
96	 2827
97	 3911
98	 6097
99	 12533
100	 56702

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 82120
# unique Features these remaining alignments represent: 69159
% of total features these alignments represent : 80.68 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 69987
2000	 8726
3000	 2048
4000	 595
5000	 180
6000	 126
7000	 102
8000	 25
9000	 21
10000	 16
20000	 123

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 81356
# unique Features these remaining alignments represent: 68446
% of total features these alignments represent : 79.85 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 10
95	 116
96	 346
97	 1273
98	 5980
99	 30578
100	 43053

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 65974
2	 2140
3	 200
4	 61
5	 18
6	 5
8	 6
9	 1
10	 2
20	 7
30	 0
40	 0
50	 1
100	 2

 Features that hit more than four times are deleted.  
# remaining Alignments : 71098
# unique Features these remaining alignments represent: 68375
% of total features these alignments represent : 79.77 %
  

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