This reports the protocol used to align the RicePunctata_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 14:50:14 2006


Source of RicePunctata_BACend_OMAP : from Gramene markers database, originally Downloaded from genbank nucleotide databse with keyword 'OP__Ba'   

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

68384 RicePunctata_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 : 93229
# unique Features these alignments represent: 64422
% of total features these alignments represent : 94.21 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 3078
150	 3455
200	 4537
250	 4906
300	 5247
350	 5375
400	 5237
450	 5511
500	 6103
550	 7120
600	 7876
650	 9213
700	 9054
750	 7544
800	 5224
10000	 3749

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 90206
# unique Features these remaining alignments represent: 61844
% of total features these alignments represent : 90.44 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 74647
2000	 897
3000	 429
4000	 345
5000	 288
6000	 204
7000	 179
8000	 112
9000	 77
10000	 90
20000	 668

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 76318
# unique Features these remaining alignments represent: 53061
% of total features these alignments represent : 77.59 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 45483
2	 3919
3	 1257
4	 650
5	 419
6	 260
8	 483
9	 109
10	 109
20	 274
30	 43
40	 20
50	 22
100	 13

 Features that hit more than thrice are deleted. 
# remaining Alignments : 57092
# unique Features these remaining alignments represent: 50659
% of total features these alignments represent : 74.08 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 2
40	 12
50	 70
60	 340
70	 1325
80	 4895
90	 17126
100	 33322

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 56734
# unique Features these remaining alignments represent: 50349
% of total features these alignments represent : 73.63 %

Following is the final summary
# alignments : 56734
# unique Features these alignments represent: 50349
% of total features these alignments represent : 73.63 %