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


Source of RiceJaponica_cDNA_KOME : from Gramene markers database, originally Downloaded from Genbank with query 'FLI_CDNA[Keyword] AND Oryza[Organism] AND Kikuchi[Author]' 

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

32127 RiceJaponica_cDNA_KOME are aligned to tigrv4-genome 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 : 31511
# unique Features these alignments represent: 30670
% of total features these alignments represent : 95.46 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 16
19	 63
29	 31
39	 58
49	 47
59	 233
69	 205
79	 174
89	 219
90	 24
91	 16
92	 30
93	 30
94	 27
95	 31
96	 44
97	 66
98	 102
99	 270
100	 29825

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 30307
# unique Features these remaining alignments represent: 29869
% of total features these alignments represent : 92.97 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 14106
2000	 6472
3000	 4509
4000	 2318
5000	 1105
6000	 635
7000	 366
8000	 241
9000	 174
10000	 102
20000	 231

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 27405
# unique Features these remaining alignments represent: 26989
% of total features these alignments represent : 84.01 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 0
95	 0
96	 1
97	 5
98	 9
99	 12984
100	 14406

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 26806
2	 105
3	 27
4	 14
5	 11
6	 17
8	 5
9	 1
10	 1
20	 1
30	 1
40	 0
50	 0
100	 0

 Features that hit more than four times are deleted.  
# remaining Alignments : 27153
# unique Features these remaining alignments represent: 26952
% of total features these alignments represent : 83.89 %