This reports the protocol used to align the Maize_ArrayConsensus_Affy18K features to Maize_BACs_20060126.
Fri Feb 24 09:57:27 2006


Source of Maize_ArrayConsensus_Affy18K : NULL 

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

17555 Maize_ArrayConsensus_Affy18K are aligned to Maize_BACs_20060126 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 : 3463
# unique Features these alignments represent: 2647
% of total features these alignments represent : 15.08 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 75
19	 298
29	 312
39	 317
49	 337
59	 245
69	 140
79	 211
89	 370
90	 48
91	 71
92	 88
93	 97
94	 95
95	 141
96	 173
97	 126
98	 118
99	 77
100	 124

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 619
# unique Features these remaining alignments represent: 490
% of total features these alignments represent : 2.79 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 419
2000	 69
3000	 58
4000	 18
5000	 21
6000	 1
7000	 7
8000	 5
9000	 7
10000	 3
20000	 8

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 564
# unique Features these remaining alignments represent: 444
% of total features these alignments represent : 2.53 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 0
95	 40
96	 9
97	 25
98	 55
99	 251
100	 184

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 380
2	 41
3	 15
4	 2
5	 1
6	 3
8	 0
9	 1
10	 0
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than four times are deleted.  
# remaining Alignments : 515
# unique Features these remaining alignments represent: 438
% of total features these alignments represent : 2.50 %