This reports the protocol used to align the Rice_FSTtos17 features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 15:28:01 2007


Source of Rice_FSTtos17 : Downloaded from genbank using the query 'txid4530[orgn] AND tos17[TITL] AND GSS[KYWD]' 

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

18024 Rice_FSTtos17 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 : 18234
# unique Features these alignments represent: 17357
% of total features these alignments represent : 96.30 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 12108
1	 1794
2	 982
3	 645
4	 320
5	 247
6	 192
7	 156
8	 140
9	 102
10	 115
20	 434
30	 196
40	 104
50	 75
60	 39
70	 24
80	 22
90	 23
100	 18
200	 112
300	 62
400	 44
500	 41
600	 4
700	 7
800	 11
900	 3
10000	 111

Features with gaps > 40 bp are deleted 
# remaining Alignments : 17535
# unique Features these remaining alignments represent: 16700
% of total features these alignments represent : 92.65 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 0
29	 3
39	 24
49	 36
59	 92
69	 109
79	 288
89	 1006
90	 226
91	 221
92	 292
93	 366
94	 461
95	 603
96	 821
97	 1182
98	 1763
99	 2897
100	 7145

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 15758
# unique Features these remaining alignments represent: 15043
% of total features these alignments represent : 83.46 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 5
91	 8
92	 10
93	 28
94	 42
95	 77
96	 161
97	 368
98	 1571
99	 8339
100	 5149

 Features less than 92 % identity are deleted. 
# remaining Alignments : 15745
# unique Features these remaining alignments represent: 15031
% of total features these alignments represent : 83.39 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 14423
2	 538
3	 43
4	 25
5	 1
6	 0
8	 0
9	 0
10	 0
20	 1
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 15628
# unique Features these remaining alignments represent: 15004
% of total features these alignments represent : 83.24 %
  

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