This reports the protocol used to align the Rice_MarkerRFLP features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 20:12:06 2007


Source of Rice_MarkerRFLP : Obtained from Gramene Marker database 

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

4333 Rice_MarkerRFLP are aligned to Oryza_sativa_indica-chromosome-20070724 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 : 4301
# unique Features these alignments represent: 4137
% of total features these alignments represent : 95.48 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 0
19	 0
29	 0
39	 6
49	 9
59	 28
69	 87
79	 185
89	 452
90	 95
91	 123
92	 160
93	 188
94	 256
95	 283
96	 397
97	 405
98	 372
99	 455
100	 800

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 2432
# unique Features these remaining alignments represent: 2344
% of total features these alignments represent : 54.10 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 2064
2000	 230
3000	 66
4000	 26
5000	 6
6000	 7
7000	 4
8000	 2
9000	 0
10000	 0
20000	 8

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 2386
# unique Features these remaining alignments represent: 2302
% of total features these alignments represent : 53.13 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 2
95	 2
96	 14
97	 37
98	 268
99	 1183
100	 880

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2234
2	 56
3	 8
4	 4
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 : 2386
# unique Features these remaining alignments represent: 2302
% of total features these alignments represent : 53.13 %
  

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