This reports the protocol used to align the RiceIndica_EST_BGI features to tigrv4-genome.
Fri Apr 14 12:01:39 2006


Source of RiceIndica_EST_BGI : Oryza indica ESTs from Gramene markers database, originally downloaded from http://btn.genomics.org.cn/ 

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

85719 RiceIndica_EST_BGI are aligned to tigrv4-genome 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 : 86501
# unique Features these alignments represent: 81219
% of total features these alignments represent : 94.75 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 0
19	 0
29	 18
39	 109
49	 151
59	 361
69	 470
79	 739
89	 2796
90	 725
91	 782
92	 979
93	 1183
94	 1579
95	 2302
96	 3171
97	 4536
98	 7226
99	 14384
100	 44990

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 74365
# unique Features these remaining alignments represent: 69808
% of total features these alignments represent : 81.44 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 62173
2000	 8939
3000	 2053
4000	 663
5000	 190
6000	 90
7000	 71
8000	 42
9000	 26
10000	 13
20000	 79

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 73828
# unique Features these remaining alignments represent: 69307
% of total features these alignments represent : 80.85 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 11
95	 143
96	 513
97	 1872
98	 7994
99	 35638
100	 27657

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 67848
2	 730
3	 241
4	 87
5	 50
6	 74
8	 208
9	 41
10	 9
20	 11
30	 1
40	 1
50	 3
100	 2

 Features that hit more than four times are deleted.  
# remaining Alignments : 70379
# unique Features these remaining alignments represent: 68906
% of total features these alignments represent : 80.39 %