This reports the protocol used to align the RiceRidleyi_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 18:15:35 2006


Source of RiceRidleyi_BACend_OMAP : from Gramene markers database, type GSS, species Oryza ridleyi 

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

204729 RiceRidleyi_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 : 169637
# unique Features these alignments represent: 133675
% of total features these alignments represent : 65.29 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 31983
150	 19797
200	 13944
250	 12848
300	 12380
350	 12680
400	 12530
450	 12035
500	 11273
550	 9425
600	 7893
650	 5925
700	 3730
750	 2015
800	 753
10000	 426

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 138098
# unique Features these remaining alignments represent: 108435
% of total features these alignments represent : 52.97 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 124224
2000	 547
3000	 277
4000	 188
5000	 126
6000	 209
7000	 212
8000	 122
9000	 82
10000	 89
20000	 813

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 125236
# unique Features these remaining alignments represent: 99479
% of total features these alignments represent : 48.59 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 86678
2	 8118
3	 2137
4	 936
5	 541
6	 287
8	 439
9	 92
10	 60
20	 165
30	 14
40	 6
50	 5
100	 1

 Features that hit more than thrice are deleted. 
# remaining Alignments : 109325
# unique Features these remaining alignments represent: 96933
% of total features these alignments represent : 47.35 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 8
30	 60
40	 315
50	 1487
60	 5320
70	 12711
80	 15961
90	 33733
100	 39730

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 103060
# unique Features these remaining alignments represent: 91810
% of total features these alignments represent : 44.84 %

Following is the final summary
# alignments : 103060
# unique Features these alignments represent: 91810
% of total features these alignments represent : 44.84 %