This reports the protocol used to align the Maize_MAGI_ISU features to tigrv4-genome.
Fri Apr 14 18:32:32 2006


Source of Maize_MAGI_ISU : Maize_ISU_MAGIs_3_1_w_singleton : from Gramene markers database, originally Downloaded from http://magi.plantgenomics.iastate.edu/downloadall.html 

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

192954 Maize_MAGI_ISU 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 : 69237
# unique Features these alignments represent: 48758
% of total features these alignments represent : 25.27 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 20945
150	 8863
200	 7329
250	 5872
300	 4537
350	 3801
400	 3023
450	 2487
500	 1928
550	 1635
600	 1355
650	 1090
700	 902
750	 843
800	 740
10000	 3887

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 48527
# unique Features these remaining alignments represent: 37742
% of total features these alignments represent : 19.56 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 42911
2000	 2701
3000	 758
4000	 296
5000	 183
6000	 86
7000	 87
8000	 69
9000	 67
10000	 42
20000	 301

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 46666
# unique Features these remaining alignments represent: 36239
% of total features these alignments represent : 18.78 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 35420
2	 679
3	 78
4	 31
5	 12
6	 2
8	 7
9	 3
10	 0
20	 6
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 37012
# unique Features these remaining alignments represent: 36177
% of total features these alignments represent : 18.75 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 3
30	 32
40	 155
50	 362
60	 636
70	 1184
80	 4345
90	 23136
100	 7159

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 35919
# unique Features these remaining alignments represent: 35169
% of total features these alignments represent : 18.23 %

Following is the final summary
# alignments : 35919
# unique Features these alignments represent: 35169
% of total features these alignments represent : 18.23 %