This reports the protocol used to align the Rice_ESTcluster_TIGR features to Oryza_sativa_indica-chromosome-20070724.
Tue Aug  7 18:43:44 2007


Source of Rice_ESTcluster_TIGR : Downloaded from TIGR at ftp://ftp.tigr.org/pub/data/tgi/Oryza_sativa/OGI.release_16.zip 

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

36381 Rice_ESTcluster_TIGR 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 : 36685
# unique Features these alignments represent: 34619
% of total features these alignments represent : 95.16 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 13
19	 60
29	 92
39	 125
49	 238
59	 531
69	 713
79	 966
89	 1775
90	 327
91	 345
92	 412
93	 567
94	 791
95	 937
96	 1372
97	 1919
98	 2749
99	 5175
100	 17577

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 28802
# unique Features these remaining alignments represent: 27506
% of total features these alignments represent : 75.61 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 13936
2000	 5455
3000	 3623
4000	 1904
5000	 1071
6000	 636
7000	 396
8000	 242
9000	 193
10000	 139
20000	 526

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 24918
# unique Features these remaining alignments represent: 23965
% of total features these alignments represent : 65.87 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 5
95	 219
96	 511
97	 1109
98	 2700
99	 17303
100	 3071

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 23416
2	 409
3	 61
4	 37
5	 19
6	 11
8	 5
9	 1
10	 1
20	 3
30	 1
40	 0
50	 0
100	 1

 Features that hit more than four times are deleted.  
# remaining Alignments : 24565
# unique Features these remaining alignments represent: 23923
% of total features these alignments represent : 65.76 %
  

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