This reports the protocol used to align the RiceIndica_ESTcluster_BGI features to tigrv4-genome.
Fri Apr 14 11:58:11 2006


Source of RiceIndica_ESTcluster_BGI : Oryza indica clusters from Gramene markers database, originally downloaded from http://btn.genomics.org.cn/ 

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

23559 RiceIndica_ESTcluster_BGI 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 : 23444
# unique Features these alignments represent: 22410
% of total features these alignments represent : 95.12 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 0
19	 0
29	 4
39	 23
49	 53
59	 144
69	 184
79	 286
89	 465
90	 79
91	 110
92	 128
93	 143
94	 190
95	 283
96	 379
97	 620
98	 1270
99	 2959
100	 16124

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 21359
# unique Features these remaining alignments represent: 20552
% of total features these alignments represent : 87.24 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 16069
2000	 3116
3000	 1264
4000	 478
5000	 185
6000	 82
7000	 48
8000	 27
9000	 19
10000	 13
20000	 27

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 20927
# unique Features these remaining alignments represent: 20145
% of total features these alignments represent : 85.51 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 2
95	 37
96	 140
97	 504
98	 1810
99	 10916
100	 7518

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 19850
2	 215
3	 29
4	 14
5	 6
6	 12
8	 9
9	 2
10	 0
20	 2
30	 1
40	 2
50	 1
100	 2

 Features that hit more than four times are deleted.  
# remaining Alignments : 20423
# unique Features these remaining alignments represent: 20108
% of total features these alignments represent : 85.35 %