This reports the protocol used to align the Rice_est features to Oryza_sativa_indica-chromosome-20070724.
Sun Aug 12 12:30:04 2007


Source of Rice_est :  

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

1303983 Rice_est 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
# aligments : 1307914
# unique Features these alignments represent: 1212852
% of total features these alignments represent : 93.01 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9		3
19		631
29		2283
39		3977
49		6316
59		12945
69		20368
79		26849
89		63904
90		14433
91		16655
92		21542
93		27770
94		38045
95		49060
96		64183
97		84407
98		117135
99		203754
100		533653

Alignments less than 95 % coverage are deleted
# remaining Aligments : 1004244
# unique Features these represent alignments represent: 923818
% of total features these alignments represent : 70.85 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000		863474
2000		95618
3000		24451
4000		7138
5000		2463
6000		1701
7000		1263
8000		438
9000		316
10000		382
20000		2072

Alignments with gaps > 4000 bp are deleted
# remaining Aligments : 990681
# unique Features these represent alignments represent: 910999
% of total features these alignments represent : 69.86 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90		0
91		0
92		0
93		0
94		160
95		2655
96		10538
97		32634
98		113619
99		538877
100		292198

Frequency distribution of the remaining features
# hits	# features
--------	--------
1		879686
2		27685
3		1917
4		634
5		185
6		74
8		54
9		21
10		14
20		311
30		91
40		125
50		51
100		37

Features that hit more than four times are deleted.  
# remaining Aligments : 943343
# unique Features these represent alignments represent: 909922
% of total features these alignments represent : 69.78 %
  

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