This reports the protocol used to align the Rice_BAC features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 22:29:08 2007


Source of Rice_BAC : Downloaded from NCBI Genbank 

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

668 Rice_BAC are aligned to Oryza_sativa_indica-chromosome-20070724 using blat with blat parameters -minScore=160 followed by PslReps with -minAli=0.90 -nearTop=0.01 -singleHit. This was followed by a filtering procedure described below and applied in general to 'Same Species Genomic' data sets.

Initial summary
# alignments : 677
# unique Features these alignments represent: 667
% of total features these alignments represent : 99.85 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 6
1	 3
2	 6
3	 1
4	 3
5	 1
6	 0
7	 1
8	 0
9	 0
10	 0
20	 2
30	 2
40	 2
50	 1
60	 2
70	 0
80	 1
90	 1
100	 0
200	 8
300	 5
400	 7
500	 6
600	 1
700	 4
800	 1
900	 5
10000	 97

Features with gaps > 40 bp are deleted 
# remaining Alignments : 27
# unique Features these remaining alignments represent: 24
% of total features these alignments represent : 3.59 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 0
29	 3
39	 0
49	 1
59	 0
69	 0
79	 0
89	 1
90	 0
91	 0
92	 0
93	 0
94	 0
95	 0
96	 0
97	 0
98	 1
99	 2
100	 19

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 22
# unique Features these remaining alignments represent: 21
% of total features these alignments represent : 3.14 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 0
95	 0
96	 0
97	 0
98	 0
99	 20
100	 2

 Features less than 92 % identity are deleted. 
# remaining Alignments : 22
# unique Features these remaining alignments represent: 21
% of total features these alignments represent : 3.14 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 20
2	 1
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 thrice are deleted.  
# remaining Alignments : 22
# unique Features these remaining alignments represent: 21
% of total features these alignments represent : 3.14 %
  

Last modified: Thu Sep 13 15:01:03 2007