This reports the protocol used to align the Rice_FSTtos17 features to tigrv4-genome.
Fri Apr 14 11:57:14 2006


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

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

18024 Rice_FSTtos17 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 : 18366
# unique Features these alignments represent: 17908
% of total features these alignments represent : 99.36 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 14264
1	 1477
2	 686
3	 477
4	 230
5	 158
6	 145
7	 105
8	 83
9	 69
10	 71
20	 281
30	 98
40	 47
50	 21
60	 14
70	 8
80	 5
90	 3
100	 9
200	 30
300	 21
400	 27
500	 26
600	 0
700	 0
800	 0
900	 0
10000	 8

Features with gaps > 40 bp are deleted 
# remaining Alignments : 18191
# unique Features these remaining alignments represent: 17746
% of total features these alignments represent : 98.46 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 0
29	 0
39	 5
49	 12
59	 53
69	 53
79	 217
89	 794
90	 168
91	 186
92	 233
93	 316
94	 367
95	 500
96	 699
97	 943
98	 1563
99	 2460
100	 9622

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 16897
# unique Features these remaining alignments represent: 16503
% of total features these alignments represent : 91.56 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 2
94	 1
95	 3
96	 19
97	 70
98	 459
99	 4953
100	 11390

 Features less than 92 % identity are deleted. 
# remaining Alignments : 16897
# unique Features these remaining alignments represent: 16503
% of total features these alignments represent : 91.56 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 16163
2	 295
3	 42
4	 2
5	 0
6	 0
8	 0
9	 0
10	 1
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 16879
# unique Features these remaining alignments represent: 16500
% of total features these alignments represent : 91.54 %