This reports the protocol used to align the nonRice_MarkerRFLP features to tigrv4-genome.
Fri Apr 14 11:43:43 2006


Source of nonRice_MarkerRFLP : These are obtained from Cornell 

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

1897 nonRice_MarkerRFLP are aligned to tigrv4-genome using blat with blat parameters -minIdentity=50 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'CrossSpecies-Coding' data sets.

Initial summary
# alignments : 902
# unique Features these alignments represent: 856
% of total features these alignments represent : 45.12 %

The length of the matches are distributed as follows 
Hit_Length	# alignments
--------	--------
100	 187
150	 139
200	 169
250	 95
300	 85
350	 58
400	 46
450	 47
500	 27
550	 16
600	 10
650	 4
700	 4
750	 4
800	 1
10000	 10

Alignments with matches less than 150 bp are deleted
# remaining Alignments : 578
# unique Features these remaining alignments represent: 545
% of total features these alignments represent : 28.73 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 523
2	 18
3	 1
4	 1
5	 0
6	 2
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 : 562
# unique Features these remaining alignments represent: 542
% of total features these alignments represent : 28.57 %

% Identity distribution of the remaining features
% Identity	# features
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 1
60	 2
70	 6
80	 41
90	 383
95	 123
100	 6

Following is the distribution of gaps
Gaps	# features
--------	--------
1000	 507
2000	 31
3000	 10
4000	 3
5000	 1
6000	 1
7000	 0
8000	 1
9000	 0
10000	 1

Following is the final summary
# alignments : 562
# unique Features these alignments represent: 542
% of total features these alignments represent : 28.57 %