This reports the protocol used to align the Rice_FSTtransposon features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 18:41:36 2007


Source of Rice_FSTtransposon : UCD FSTs downloaded from genebank using "transposon AND insertion lines AND oryza[Organism]"   

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

4183 Rice_FSTtransposon 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 : 3618
# unique Features these alignments represent: 3297
% of total features these alignments represent : 78.82 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 1936
1	 376
2	 163
3	 115
4	 78
5	 67
6	 47
7	 47
8	 29
9	 27
10	 33
20	 202
30	 135
40	 64
50	 29
60	 26
70	 21
80	 13
90	 10
100	 10
200	 51
300	 20
400	 12
500	 12
600	 1
700	 0
800	 0
900	 0
10000	 15

Features with gaps > 40 bp are deleted 
# remaining Alignments : 3319
# unique Features these remaining alignments represent: 3026
% of total features these alignments represent : 72.34 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 0
29	 4
39	 20
49	 77
59	 139
69	 205
79	 252
89	 429
90	 84
91	 79
92	 90
93	 105
94	 110
95	 127
96	 157
97	 207
98	 196
99	 345
100	 693

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 2113
# unique Features these remaining alignments represent: 1958
% of total features these alignments represent : 46.81 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 4
91	 5
92	 5
93	 12
94	 29
95	 41
96	 113
97	 143
98	 431
99	 817
100	 513

 Features less than 92 % identity are deleted. 
# remaining Alignments : 2104
# unique Features these remaining alignments represent: 1950
% of total features these alignments represent : 46.62 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 1860
2	 71
3	 13
4	 0
5	 3
6	 0
8	 0
9	 0
10	 1
20	 1
30	 1
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 2041
# unique Features these remaining alignments represent: 1944
% of total features these alignments represent : 46.47 %
  

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