This reports the protocol used to align the Maize_cornsensus features to Maize_BACs.
 Kiran Ratnapu 
Tue Mar 29 16:53:05 2005


Source of Maize_cornsensus : These are obtained from Mary Polacco  

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

10678 Maize_cornsensus 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 : 1541
# unique Features these alignments represent: 1308
% of total features these alignments represent : 12.25 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 33
19	 159
29	 133
39	 127
49	 105
59	 119
69	 150
79	 166
89	 132
90	 20
91	 17
92	 15
93	 16
94	 28
95	 38
96	 41
97	 39
98	 72
99	 68
100	 63

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 283
# unique Features these remaining alignments represent: 258
% of total features these alignments represent : 2.42 %

RICE_GAP distribution of the remaining features
Rice_Gaps	# alignments
--------	--------
1000	 144
2000	 50
3000	 35
4000	 19
5000	 13
6000	 8
7000	 2
8000	 3
9000	 2
10000	 2
20000	 3

Alignments with gaps on rice > 4000 bp are deleted
# remaining Alignments : 248
# unique Features these remaining alignments represent: 224
% of total features these alignments represent : 2.10 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 0
95	 0
96	 3
97	 7
98	 26
99	 111
100	 101

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 201
2	 22
3	 1
4	 0
5	 0
6	 0
8	 0
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 : 248
# unique Features these remaining alignments represent: 224
% of total features these alignments represent : 2.10 %