This reports the protocol used to align the RiceMinuta_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 16:52:18 2006


Source of RiceMinuta_BACend_OMAP : from Gramene markers database, originally From genbank Nucleotide database with keyword 'OM__Ba'  

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

169651 RiceMinuta_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 : 215500
# unique Features these alignments represent: 152250
% of total features these alignments represent : 89.74 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 10738
150	 12209
200	 14809
250	 15844
300	 16689
350	 18006
400	 18665
450	 20002
500	 20869
550	 20730
600	 19252
650	 13729
700	 8166
750	 3868
800	 1368
10000	 556

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 204996
# unique Features these remaining alignments represent: 143532
% of total features these alignments represent : 84.60 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 179234
2000	 1307
3000	 642
4000	 617
5000	 276
6000	 290
7000	 208
8000	 173
9000	 301
10000	 151
20000	 1142

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 181800
# unique Features these remaining alignments represent: 128302
% of total features these alignments represent : 75.63 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 109994
2	 10414
3	 2799
4	 1331
5	 843
6	 550
8	 985
9	 248
10	 181
20	 703
30	 153
40	 49
50	 31
100	 21

 Features that hit more than thrice are deleted. 
# remaining Alignments : 139219
# unique Features these remaining alignments represent: 123207
% of total features these alignments represent : 72.62 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 1
30	 10
40	 70
50	 260
60	 894
70	 4188
80	 14951
90	 47711
100	 71134

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 138138
# unique Features these remaining alignments represent: 122243
% of total features these alignments represent : 72.06 %

Following is the final summary
# alignments : 138138
# unique Features these alignments represent: 122243
% of total features these alignments represent : 72.06 %