This reports the protocol used to align the Sorghum_GSS_Klein features to tigrv4-genome.
Fri Apr 14 11:50:07 2006


Source of Sorghum_GSS_Klein : from Gramene markers database, originally These are from Patricia Klein 

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

172 Sorghum_GSS_Klein 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 : 140
# unique Features these alignments represent: 139
% of total features these alignments represent : 80.81 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 17
150	 29
200	 18
250	 24
300	 15
350	 14
400	 10
450	 3
500	 4
550	 1
600	 4
650	 1
700	 0
750	 0
800	 0
10000	 0

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 124
# unique Features these remaining alignments represent: 124
% of total features these alignments represent : 72.09 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 122
2000	 0
3000	 0
4000	 1
5000	 0
6000	 1
7000	 0
8000	 0
9000	 0
10000	 0
20000	 0

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 123
# unique Features these remaining alignments represent: 123
% of total features these alignments represent : 71.51 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 123
2	 0
3	 0
4	 0
5	 0
6	 0
8	 0
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 123
# unique Features these remaining alignments represent: 123
% of total features these alignments represent : 71.51 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 0
40	 0
50	 0
60	 0
70	 2
80	 14
90	 85
100	 22

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 123
# unique Features these remaining alignments represent: 123
% of total features these alignments represent : 71.51 %

Following is the final summary
# alignments : 123
# unique Features these alignments represent: 123
% of total features these alignments represent : 71.51 %