This reports the protocol used to align the RiceRufipogon_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 15:29:46 2006


Source of RiceRufipogon_BACend_OMAP : from Gramene markers database, originally From genbank Nucleotide database with keyword 'OR_CBa'   

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

70982 RiceRufipogon_BACend_OMAP 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 : 150483
# unique Features these alignments represent: 69141
% of total features these alignments represent : 97.41 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 82651
1	 20406
2	 8061
3	 4337
4	 2609
5	 2091
6	 1816
7	 1558
8	 1110
9	 880
10	 801
20	 4682
30	 2123
40	 1090
50	 992
60	 537
70	 508
80	 280
90	 220
100	 157
200	 1730
300	 860
400	 624
500	 478
600	 177
700	 106
800	 143
900	 68
10000	 2175

Features with gaps > 40 bp are deleted 
# remaining Alignments : 134215
# unique Features these remaining alignments represent: 62451
% of total features these alignments represent : 87.98 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 0
29	 76
39	 186
49	 238
59	 465
69	 627
79	 667
89	 1664
90	 564
91	 626
92	 930
93	 1369
94	 2026
95	 3508
96	 7269
97	 12415
98	 19306
99	 36000
100	 46279

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 129734
# unique Features these remaining alignments represent: 59611
% of total features these alignments represent : 83.98 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 89
91	 203
92	 357
93	 711
94	 1618
95	 4902
96	 10414
97	 16343
98	 34663
99	 55047
100	 5387

 Features less than 92 % identity are deleted. 
# remaining Alignments : 129442
# unique Features these remaining alignments represent: 59484
% of total features these alignments represent : 83.80 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 49768
2	 2303
3	 1468
4	 1232
5	 806
6	 516
8	 1331
9	 248
10	 248
20	 844
30	 257
40	 203
50	 82
100	 130

 Features that hit more than thrice are deleted.  
# remaining Alignments : 58778
# unique Features these remaining alignments represent: 53539
% of total features these alignments represent : 75.43 %