This reports the protocol used to align the Rice_EST features to tigrv4-genome.
Mon Apr 17 15:31:38 2006


Source of Rice_EST : from Gramene markers database, originally Downloaded from Genbank with query 'txid4530[orgn]  AND  gbdiv_est[PROP] 

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

1274663 Rice_EST 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
# aligments : 1310558
# unique Features these alignments represent: 1215951
% of total features these alignments represent : 95.39 %

The following is the distribution of the feature coverage 
%coverage	no of alignments
--------	--------
9		1
19		211
29		1126
39		2677
49		4521
59		10055
69		17380
79		22534
89		54857
90		12561
91		14733
92		19170
93		24271
94		33034
95		43478
96		57253
97		76841
98		101990
99		165509
100		648349

Alignments less than 95 % coverage are deleted
# remaining Aligments : 1050919
# unique Features these represent alignments represent: 980222
% of total features these alignments represent : 76.90 %

GAP distribution of the remaining features
Gaps	# alignments
--------	--------
1000		909693
2000		101381
3000		25253
4000		7916
5000		2607
6000		1220
7000		821
8000		383
9000		280
10000		219
20000		719

Alignments with gaps > 4000 bp are deleted
# remaining Aligments : 1044243
# unique Features these represent alignments represent: 973921
% of total features these alignments represent : 76.41 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90		0
91		0
92		0
93		0
94		118
95		1893
96		8316
97		22781
98		72158
99		464285
100		474692

Frequency distribution of the remaining features
# hits	# features
--------	--------
1		950535
2		12690
3		1991
4		1433
5		1154
6		1128
8		4281
9		464
10		67
20		108
30		15
40		14
50		11
100		16

Features that hit more than four times are deleted.  
# remaining Aligments : 987620
# unique Features these represent alignments represent: 966649
% of total features these alignments represent : 75.84 %