This reports the protocol used to align the Maize_consensus_Affymetrix features to Maize_BACs.
 Kiran Ratnapu 
Tue May 31 16:18:53 2005


Source of Maize_consensus_Affymetrix : Downloaded from Affymetrix website  

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

17555 Maize_consensus_Affymetrix are aligned to Maize_BACs 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 : 2829
# unique Features these alignments represent: 2147
% of total features these alignments represent : 12.23 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 60
19	 201
29	 205
39	 230
49	 231
59	 185
69	 108
79	 150
89	 336
90	 47
91	 65
92	 88
93	 90
94	 92
95	 143
96	 167
97	 123
98	 109
99	 77
100	 122

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 599
# unique Features these remaining alignments represent: 476
% of total features these alignments represent : 2.71 %

RICE_GAP distribution of the remaining features
Rice_Gaps	# alignments
--------	--------
1000	 406
2000	 63
3000	 56
4000	 20
5000	 17
6000	 3
7000	 8
8000	 4
9000	 7
10000	 4
20000	 8

Alignments with gaps on rice > 4000 bp are deleted
# remaining Alignments : 545
# unique Features these remaining alignments represent: 430
% of total features these alignments represent : 2.45 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 0
95	 40
96	 8
97	 21
98	 53
99	 242
100	 181

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 366
2	 45
3	 12
4	 1
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 : 496
# unique Features these remaining alignments represent: 424
% of total features these alignments represent : 2.42 %