This reports the protocol used to align the Rice_MarkerRFLP features to tigrv4-genome.
Fri Apr 14 11:50:31 2006


Source of Rice_MarkerRFLP : Obtained from Gramene Marker database 

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

4333 Rice_MarkerRFLP are aligned to tigrv4-genome 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 : 4377
# unique Features these alignments represent: 4252
% of total features these alignments represent : 98.13 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 0
19	 0
29	 0
39	 3
49	 5
59	 23
69	 76
79	 165
89	 392
90	 71
91	 108
92	 159
93	 172
94	 218
95	 297
96	 406
97	 465
98	 362
99	 471
100	 984

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 2693
# unique Features these remaining alignments represent: 2594
% of total features these alignments represent : 59.87 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 2316
2000	 263
3000	 72
4000	 26
5000	 5
6000	 4
7000	 4
8000	 1
9000	 1
10000	 0
20000	 1

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 2677
# unique Features these remaining alignments represent: 2579
% of total features these alignments represent : 59.52 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 0
95	 1
96	 8
97	 25
98	 160
99	 1066
100	 1417

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2518
2	 46
3	 7
4	 1
5	 4
6	 0
8	 3
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 : 2635
# unique Features these remaining alignments represent: 2572
% of total features these alignments represent : 59.36 %