This reports the protocol used to align the RiceJaponica_BACend_OMAP features to Oryza_sativa_indica-chromosome-20070724.
Wed Aug  8 10:04:35 2007


Source of RiceJaponica_BACend_OMAP : Downloaded from genbank using the query '(CUGI Rice BAC end) AND (oryza [ORGN])' and only high quality sequence is extracted based on the information from genbank records   

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

328959 RiceJaponica_BACend_OMAP 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 : 394178
# unique Features these alignments represent: 304416
% of total features these alignments represent : 92.54 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 153408
1	 38854
2	 20617
3	 12771
4	 9301
5	 7595
6	 7069
7	 6581
8	 5888
9	 5101
10	 4719
20	 27781
30	 12868
40	 7725
50	 5222
60	 3671
70	 2779
80	 2178
90	 1990
100	 1668
200	 7123
300	 4015
400	 3233
500	 2411
600	 1470
700	 1306
800	 1253
900	 1082
10000	 17294

Features with gaps > 40 bp are deleted 
# remaining Alignments : 320278
# unique Features these remaining alignments represent: 249594
% of total features these alignments represent : 75.87 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 2
19	 187
29	 4442
39	 9326
49	 13854
59	 21989
69	 31426
79	 34238
89	 45885
90	 6087
91	 6787
92	 7122
93	 7848
94	 8328
95	 8438
96	 9090
97	 12067
98	 16790
99	 23638
100	 52734

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 152985
# unique Features these remaining alignments represent: 122343
% of total features these alignments represent : 37.19 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 185
91	 273
92	 547
93	 1045
94	 2122
95	 4021
96	 8392
97	 17221
98	 33965
99	 51506
100	 33708

 Features less than 92 % identity are deleted. 
# remaining Alignments : 152527
# unique Features these remaining alignments represent: 121994
% of total features these alignments represent : 37.08 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 111396
2	 5779
3	 1693
4	 967
5	 616
6	 382
8	 420
9	 128
10	 130
20	 367
30	 75
40	 23
50	 5
100	 9

 Features that hit more than thrice are deleted.  
# remaining Alignments : 128033
# unique Features these remaining alignments represent: 118868
% of total features these alignments represent : 36.13 %
  

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