This reports the protocol used to align the RiceCoarctata_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 17:18:54 2006


Source of RiceCoarctata_BACend_OMAP : from Gramene markers database, originally From genbank Nucleotide database with keyword 'OC__Ba'  

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

195285 RiceCoarctata_BACend_OMAP are aligned to tigrv4-genome using blat with blat parameters -minIdentity=50 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'CrossSpecies-Genomic' data sets.

Initial summary
# alignments : 154825
# unique Features these alignments represent: 128110
% of total features these alignments represent : 65.60 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 21084
150	 11196
200	 10519
250	 9844
300	 9684
350	 9920
400	 10046
450	 10341
500	 10855
550	 11002
600	 10845
650	 9630
700	 7707
750	 5518
800	 3684
10000	 2950

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 134005
# unique Features these remaining alignments represent: 109868
% of total features these alignments represent : 56.26 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 129437
2000	 746
3000	 261
4000	 189
5000	 95
6000	 119
7000	 115
8000	 93
9000	 67
10000	 62
20000	 432

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 130633
# unique Features these remaining alignments represent: 107232
% of total features these alignments represent : 54.91 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 99591
2	 3273
3	 1072
4	 883
5	 609
6	 284
8	 1160
9	 107
10	 81
20	 156
30	 12
40	 1
50	 0
100	 2

 Features that hit more than thrice are deleted. 
# remaining Alignments : 109353
# unique Features these remaining alignments represent: 103936
% of total features these alignments represent : 53.22 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 3
30	 31
40	 132
50	 521
60	 2136
70	 3779
80	 6639
90	 30055
100	 66057

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 106850
# unique Features these remaining alignments represent: 101669
% of total features these alignments represent : 52.06 %

Following is the final summary
# alignments : 106850
# unique Features these alignments represent: 101669
% of total features these alignments represent : 52.06 %