This reports the protocol used to align the Rice_FST-TDNA features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 15:03:35 2007


Source of Rice_FST-TDNA : Downloaded from Genbank with query "txid4530[orgn] AND GSS[PROP] AND T-DNA insertion lines" 

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

14533 Rice_FST-TDNA 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 : 16335
# unique Features these alignments represent: 13248
% of total features these alignments represent : 91.16 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 12463
1	 951
2	 407
3	 244
4	 154
5	 118
6	 115
7	 83
8	 96
9	 59
10	 57
20	 375
30	 212
40	 102
50	 66
60	 65
70	 45
80	 34
90	 27
100	 17
200	 104
300	 100
400	 70
500	 50
600	 7
700	 4
800	 5
900	 18
10000	 104

Features with gaps > 40 bp are deleted 
# remaining Alignments : 15436
# unique Features these remaining alignments represent: 12536
% of total features these alignments represent : 86.26 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 0
29	 1
39	 16
49	 68
59	 182
69	 187
79	 283
89	 734
90	 145
91	 180
92	 220
93	 275
94	 320
95	 465
96	 570
97	 883
98	 1420
99	 2251
100	 7236

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 13828
# unique Features these remaining alignments represent: 11175
% of total features these alignments represent : 76.89 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 37
91	 28
92	 57
93	 89
94	 152
95	 258
96	 575
97	 1264
98	 2439
99	 3780
100	 5149

 Features less than 92 % identity are deleted. 
# remaining Alignments : 13763
# unique Features these remaining alignments represent: 11127
% of total features these alignments represent : 76.56 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 10537
2	 413
3	 62
4	 29
5	 16
6	 4
8	 19
9	 3
10	 6
20	 18
30	 8
40	 5
50	 1
100	 3

 Features that hit more than thrice are deleted.  
# remaining Alignments : 11549
# unique Features these remaining alignments represent: 11012
% of total features these alignments represent : 75.77 %
  

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