This reports the protocol used to align the Rice_ESTcluster_TIGR features to tigrv4-genome.
Fri Apr 14 12:25:53 2006


Source of Rice_ESTcluster_TIGR : from Gramene markers database, originally 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 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 : 38815
# unique Features these alignments represent: 35830
% of total features these alignments represent : 98.49 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9	 0
19	 24
29	 16
39	 44
49	 120
59	 417
69	 443
79	 587
89	 959
90	 153
91	 173
92	 201
93	 246
94	 331
95	 411
96	 550
97	 835
98	 1369
99	 2868
100	 29054

 Alignments less than 95 % coverage are deleted
# remaining Alignments : 34694
# unique Features these remaining alignments represent: 32374
% of total features these alignments represent : 88.99 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 18077
2000	 6579
3000	 4282
4000	 2282
5000	 1224
6000	 683
7000	 417
8000	 245
9000	 194
10000	 116
20000	 305

Alignments with gaps > 4000 bp are deleted
# remaining Alignments : 31220
# unique Features these remaining alignments represent: 29119
% of total features these alignments represent : 80.04 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 1
95	 13
96	 52
97	 220
98	 1043
99	 12471
100	 17420

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 28513
2	 360
3	 98
4	 40
5	 22
6	 14
8	 19
9	 5
10	 6
20	 27
30	 4
40	 6
50	 2
100	 2

 Features that hit more than four times are deleted.  
# remaining Alignments : 29687
# unique Features these remaining alignments represent: 29011
% of total features these alignments represent : 79.74 %