This reports the protocol used to align the RiceGranulata_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 17:59:21 2006


Source of RiceGranulata_BACend_OMAP : from Gramene markers database, type GSS, species Oryza granulata 

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

138171 RiceGranulata_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 : 120253
# unique Features these alignments represent: 87479
% of total features these alignments represent : 63.31 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 21489
150	 13409
200	 9654
250	 8547
300	 8090
350	 8554
400	 7793
450	 6867
500	 6819
550	 6295
600	 5880
650	 5719
700	 4421
750	 3369
800	 1866
10000	 1481

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 99057
# unique Features these remaining alignments represent: 70949
% of total features these alignments represent : 51.35 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 86172
2000	 361
3000	 176
4000	 158
5000	 94
6000	 106
7000	 65
8000	 96
9000	 60
10000	 73
20000	 632

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 86867
# unique Features these remaining alignments represent: 62360
% of total features these alignments represent : 45.13 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 53083
2	 5095
3	 1593
4	 813
5	 455
6	 236
8	 645
9	 90
10	 103
20	 182
30	 20
40	 18
50	 10
100	 17

 Features that hit more than thrice are deleted. 
# remaining Alignments : 68052
# unique Features these remaining alignments represent: 59771
% of total features these alignments represent : 43.26 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 3
30	 48
40	 173
50	 833
60	 3033
70	 7870
80	 10691
90	 20735
100	 24666

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 64479
# unique Features these remaining alignments represent: 56649
% of total features these alignments represent : 41.00 %

Following is the final summary
# alignments : 64479
# unique Features these alignments represent: 56649
% of total features these alignments represent : 41.00 %