This reports the protocol used to align the RiceBrachyantha_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 12:24:15 2006


Source of RiceBrachyantha_BACend_OMAP : from Gramene markers database, originally Downloaded from Genbank with 'Brachyantha' as keyword  

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

67364 RiceBrachyantha_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 : 68274
# unique Features these alignments represent: 52014
% of total features these alignments represent : 77.21 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 9215
150	 6468
200	 5179
250	 4865
300	 4770
350	 4259
400	 4521
450	 4422
500	 4368
550	 4386
600	 4220
650	 4028
700	 3522
750	 2298
800	 1269
10000	 484

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 59193
# unique Features these remaining alignments represent: 44396
% of total features these alignments represent : 65.90 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 53135
2000	 214
3000	 72
4000	 77
5000	 61
6000	 39
7000	 32
8000	 42
9000	 53
10000	 30
20000	 266

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 53498
# unique Features these remaining alignments represent: 40136
% of total features these alignments represent : 59.58 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 36002
2	 1873
3	 644
4	 416
5	 275
6	 142
8	 511
9	 47
10	 53
20	 138
30	 18
40	 2
50	 5
100	 10

 Features that hit more than thrice are deleted. 
# remaining Alignments : 41680
# unique Features these remaining alignments represent: 38519
% of total features these alignments represent : 57.18 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 1
30	 9
40	 19
50	 70
60	 310
70	 746
80	 2219
90	 15824
100	 22482

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 41317
# unique Features these remaining alignments represent: 38200
% of total features these alignments represent : 56.71 %

Following is the final summary
# alignments : 41317
# unique Features these alignments represent: 38200
% of total features these alignments represent : 56.71 %