This reports the protocol used to align the Rice_ArrayConsensus_Affy57K features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 15:38:52 2007


Source of Rice_ArrayConsensus_Affy57K : Downloaded from Affymetrix website  

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

57194 Rice_ArrayConsensus_Affy57K 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 : 54174
# unique Features these alignments represent: 52728
% of total features these alignments represent : 92.19 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 28
19	 112
29	 173
39	 253
49	 307
59	 668
69	 783
79	 1172
89	 2222
90	 425
91	 485
92	 589
93	 774
94	 951
95	 1167
96	 1730
97	 2700
98	 4555
99	 9503
100	 25577

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 44071
# unique Features these remaining alignments represent: 43201
% of total features these alignments represent : 75.53 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 23575
2000	 7845
3000	 4919
4000	 2626
5000	 1462
6000	 871
7000	 572
8000	 351
9000	 266
10000	 186
20000	 747

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 38965
# unique Features these remaining alignments represent: 38198
% of total features these alignments represent : 66.79 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 12
95	 160
96	 523
97	 1649
98	 4164
99	 25165
100	 7292

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 37543
2	 590
3	 42
4	 7
5	 12
6	 1
8	 3
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than four times are deleted.  
# remaining Alignments : 38877
# unique Features these remaining alignments represent: 38182
% of total features these alignments represent : 66.76 %
  

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