This reports the protocol used to align the Rice_CDS features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 16:25:07 2007


Source of Rice_CDS : Downloaded from Genbank with query '(txid4530[ORGN] AND complete[TITL] AND cds[TITL]) NOT (Mitochondrion[ALL] OR Chloroplast[ALL] OR Mitochondrial[ALL]) )' 

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

72229 Rice_CDS 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 : 74502
# unique Features these alignments represent: 68217
% of total features these alignments represent : 94.45 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 32
19	 130
29	 131
39	 214
49	 293
59	 665
69	 840
79	 1207
89	 2364
90	 411
91	 526
92	 590
93	 843
94	 1103
95	 1547
96	 2331
97	 3200
98	 4735
99	 9169
100	 44171

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 63618
# unique Features these remaining alignments represent: 58825
% of total features these alignments represent : 81.44 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 32951
2000	 11542
3000	 7641
4000	 3775
5000	 2012
6000	 1204
7000	 761
8000	 455
9000	 385
10000	 252
20000	 992

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 55909
# unique Features these remaining alignments represent: 52180
% of total features these alignments represent : 72.24 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 44
95	 615
96	 1382
97	 2748
98	 6006
99	 36295
100	 8819

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 50442
2	 1064
3	 272
4	 171
5	 86
6	 45
8	 40
9	 17
10	 8
20	 30
30	 3
40	 0
50	 1
100	 1

 Features that hit more than four times are deleted.  
# remaining Alignments : 54070
# unique Features these remaining alignments represent: 51949
% of total features these alignments represent : 71.92 %
  

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