This reports the protocol used to align the Rice_CDS features to tigrv4-genome.
Fri Apr 14 17:52:03 2006


Source of Rice_CDS : from Gramene markers database, originally 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 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 : 76881
# unique Features these alignments represent: 70728
% of total features these alignments represent : 97.92 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 16
19	 63
29	 33
39	 60
49	 55
59	 251
69	 229
79	 276
89	 405
90	 52
91	 66
92	 102
93	 105
94	 126
95	 210
96	 384
97	 376
98	 599
99	 1177
100	 72257

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 74836
# unique Features these remaining alignments represent: 69212
% of total features these alignments represent : 95.82 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 41980
2000	 13800
3000	 8802
4000	 4476
5000	 2220
6000	 1255
7000	 756
8000	 425
9000	 314
10000	 183
20000	 446

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 69058
# unique Features these remaining alignments represent: 63619
% of total features these alignments represent : 88.08 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 1
92	 0
93	 0
94	 0
95	 3
96	 8
97	 39
98	 237
99	 18110
100	 50660

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 62370
2	 631
3	 182
4	 110
5	 62
6	 62
8	 38
9	 15
10	 12
20	 88
30	 23
40	 13
50	 5
100	 7

 Features that hit more than four times are deleted.  
# remaining Alignments : 64618
# unique Features these remaining alignments represent: 63293
% of total features these alignments represent : 87.63 %