This reports the protocol used to align the Rice_FSTtransposon features to tigrv4-genome.
Fri Apr 14 11:52:22 2006


Source of Rice_FSTtransposon : UCD FSTs from Gramene markers database, originally downloaded from genebank using "transposon AND insertion lines AND oryza[Organism]"   

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

4183 Rice_FSTtransposon are aligned to tigrv4-genome 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 : 4162
# unique Features these alignments represent: 3476
% of total features these alignments represent : 83.10 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 2654
1	 388
2	 144
3	 96
4	 61
5	 62
6	 39
7	 45
8	 22
9	 30
10	 29
20	 154
30	 138
40	 53
50	 37
60	 54
70	 19
80	 10
90	 5
100	 13
200	 40
300	 14
400	 14
500	 13
600	 0
700	 0
800	 1
900	 0
10000	 0

Features with gaps > 40 bp are deleted 
# remaining Alignments : 3915
# unique Features these remaining alignments represent: 3294
% of total features these alignments represent : 78.75 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 0
29	 5
39	 13
49	 71
59	 168
69	 212
79	 329
89	 518
90	 89
91	 90
92	 97
93	 128
94	 103
95	 130
96	 146
97	 204
98	 182
99	 266
100	 1164

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 2513
# unique Features these remaining alignments represent: 2251
% of total features these alignments represent : 53.81 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 3
91	 8
92	 3
93	 7
94	 14
95	 31
96	 63
97	 88
98	 229
99	 721
100	 1346

 Features less than 92 % identity are deleted. 
# remaining Alignments : 2502
# unique Features these remaining alignments represent: 2240
% of total features these alignments represent : 53.55 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 2186
2	 20
3	 4
4	 0
5	 2
6	 1
8	 26
9	 0
10	 0
20	 0
30	 0
40	 0
50	 1
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 2238
# unique Features these remaining alignments represent: 2210
% of total features these alignments represent : 52.83 %