This reports the protocol used to align the Rice_ArrayConsensus_Affy57K features to tigrv4-genome.
Fri Apr 14 17:01:35 2006


Source of Rice_ArrayConsensus_Affy57K : Downloaded from Affymetrix website  

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

57194 Rice_ArrayConsensus_Affy57K 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 : 57346
# unique Features these alignments represent: 55301
% of total features these alignments represent : 96.69 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 8
19	 27
29	 24
39	 24
49	 59
59	 192
69	 184
79	 318
89	 649
90	 126
91	 209
92	 276
93	 313
94	 442
95	 500
96	 733
97	 1180
98	 2043
99	 4941
100	 45096

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 54000
# unique Features these remaining alignments represent: 52268
% of total features these alignments represent : 91.39 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 30412
2000	 9870
3000	 5995
4000	 3216
5000	 1694
6000	 992
7000	 615
8000	 361
9000	 236
10000	 149
20000	 375

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 49493
# unique Features these remaining alignments represent: 47815
% of total features these alignments represent : 83.60 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 0
95	 8
96	 39
97	 83
98	 273
99	 10337
100	 38753

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 47124
2	 402
3	 116
4	 71
5	 36
6	 22
8	 24
9	 2
10	 3
20	 8
30	 1
40	 2
50	 4
100	 0

 Features that hit more than four times are deleted.  
# remaining Alignments : 48560
# unique Features these remaining alignments represent: 47713
% of total features these alignments represent : 83.42 %