This reports the protocol used to align the Maize_CDs_panzea features to Maize_BACs.
 Kiran Ratnapu 
Tue Mar 29 17:48:22 2005


Source of Maize_CDs_panzea : Obtained from panzea project  

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

3092 Maize_CDs_panzea 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 : 423
# unique Features these alignments represent: 366
% of total features these alignments represent : 11.84 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 10
19	 42
29	 15
39	 25
49	 15
59	 8
69	 17
79	 16
89	 38
90	 12
91	 19
92	 6
93	 13
94	 19
95	 17
96	 18
97	 20
98	 37
99	 39
100	 37

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 151
# unique Features these remaining alignments represent: 135
% of total features these alignments represent : 4.37 %

RICE_GAP distribution of the remaining features
Rice_Gaps	# alignments
--------	--------
1000	 99
2000	 24
3000	 11
4000	 4
5000	 6
6000	 1
7000	 1
8000	 0
9000	 0
10000	 1
20000	 4

Alignments with gaps on rice > 4000 bp are deleted
# remaining Alignments : 138
# unique Features these remaining alignments represent: 124
% of total features these alignments represent : 4.01 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 1
95	 1
96	 1
97	 2
98	 16
99	 64
100	 53

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 110
2	 14
3	 0
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 : 138
# unique Features these remaining alignments represent: 124
% of total features these alignments represent : 4.01 %