This reports the protocol used to align the Maize_Seq_Panzea features to Maize_BACs_20060126.
Mon Feb 13 22:30:36 2006


Source of Maize_Seq_Panzea : Obtained from panzea project 

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

3092 Maize_Seq_Panzea 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 : 442
# unique Features these alignments represent: 383
% of total features these alignments represent : 12.39 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 10
19	 44
29	 16
39	 23
49	 15
59	 10
69	 21
79	 19
89	 38
90	 15
91	 18
92	 7
93	 15
94	 20
95	 16
96	 19
97	 20
98	 38
99	 39
100	 39

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 155
# unique Features these remaining alignments represent: 139
% of total features these alignments represent : 4.50 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 103
2000	 25
3000	 9
4000	 5
5000	 6
6000	 1
7000	 0
8000	 0
9000	 1
10000	 0
20000	 4

Alignments with gaps  > 4000 bp are deleted
# remaining Alignments : 142
# unique Features these remaining alignments represent: 128
% of total features these alignments represent : 4.14 %

% 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	 66
100	 55

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 114
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 : 142
# unique Features these remaining alignments represent: 128
% of total features these alignments represent : 4.14 %