This reports the protocol used to align the Rice_FST-TDNA features to tigrv4-genome.
Fri Apr 14 11:56:05 2006


Source of Rice_FST-TDNA : from Gramene markers database, originally 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 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 : 17906
# unique Features these alignments represent: 13906
% of total features these alignments represent : 95.69 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 16507
1	 363
2	 167
3	 51
4	 27
5	 25
6	 36
7	 23
8	 25
9	 17
10	 13
20	 93
30	 57
40	 48
50	 33
60	 24
70	 19
80	 22
90	 18
100	 12
200	 62
300	 35
400	 42
500	 23
600	 0
700	 0
800	 1
900	 2
10000	 68

Features with gaps > 40 bp are deleted 
# remaining Alignments : 17452
# unique Features these remaining alignments represent: 13622
% of total features these alignments represent : 93.73 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 0
29	 1
39	 5
49	 24
59	 91
69	 134
79	 173
89	 536
90	 89
91	 100
92	 166
93	 154
94	 527
95	 278
96	 436
97	 646
98	 998
99	 1364
100	 11730

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 16403
# unique Features these remaining alignments represent: 12714
% of total features these alignments represent : 87.48 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 28
91	 30
92	 28
93	 50
94	 72
95	 118
96	 276
97	 716
98	 1101
99	 3226
100	 10758

 Features less than 92 % identity are deleted. 
# remaining Alignments : 16345
# unique Features these remaining alignments represent: 12668
% of total features these alignments represent : 87.17 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 12363
2	 127
3	 34
4	 33
5	 33
6	 18
8	 11
9	 4
10	 3
20	 11
30	 11
40	 1
50	 2
100	 9

 Features that hit more than thrice are deleted.  
# remaining Alignments : 12719
# unique Features these remaining alignments represent: 12524
% of total features these alignments represent : 86.18 %