This reports the protocol used to align the RiceJaponica_cDNA_KOME features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 16:12:57 2007


Source of RiceJaponica_cDNA_KOME : Downloaded from Genbank with query 'FLI_CDNA[Keyword] AND Oryza[Organism] AND Kikuchi[Author]' 

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

32127 RiceJaponica_cDNA_KOME are aligned to Oryza_sativa_indica-chromosome-20070724 using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'Coding-SameSpecies' data sets.

Initial summary
# alignments : 30546
# unique Features these alignments represent: 30096
% of total features these alignments represent : 93.68 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 23
19	 83
29	 74
39	 98
49	 99
59	 258
69	 316
79	 430
89	 778
90	 125
91	 144
92	 157
93	 216
94	 270
95	 327
96	 417
97	 631
98	 1086
99	 2834
100	 22180

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 27152
# unique Features these remaining alignments represent: 26849
% of total features these alignments represent : 83.57 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 11954
2000	 5826
3000	 4054
4000	 2035
5000	 989
6000	 610
7000	 341
8000	 222
9000	 185
10000	 132
20000	 445

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 23869
# unique Features these remaining alignments represent: 23598
% of total features these alignments represent : 73.45 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 2
95	 15
96	 68
97	 343
98	 1189
99	 19710
100	 2542

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 23352
2	 227
3	 16
4	 2
5	 0
6	 0
8	 1
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than four times are deleted.  
# remaining Alignments : 23862
# unique Features these remaining alignments represent: 23597
% of total features these alignments represent : 73.45 %
  

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