This reports the protocol used to align the Maize_MAGI_ISU features to Maize_BACs_20060126.
Mon Feb 13 23:44:44 2006


Source of Maize_MAGI_ISU : Maize_ISU_MAGIs_3_1_w_singleton : Downloaded from http://magi.plantgenomics.iastate.edu/downloadall.html 

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

214471 Maize_MAGI_ISU are aligned to Maize_BACs_20060126 using blat with blat parameters -minScore=160 followed by PslReps with -minAli=0.90 -nearTop=0.01 -singleHit. This was followed by a filtering procedure described below and applied in general to 'Same Species Genomic' data sets.

Initial summary
# alignments : 71822
# unique Features these alignments represent: 52353
% of total features these alignments represent : 24.41 %

Following is the Gap distribution 
Gaps	# alignments
--------	--------
0	 24732
1	 5300
2	 2854
3	 1811
4	 1429
5	 1255
6	 1173
7	 1146
8	 982
9	 859
10	 790
20	 5532
30	 3185
40	 2014
50	 1438
60	 1151
70	 937
80	 700
90	 650
100	 652
200	 3197
300	 1356
400	 839
500	 552
600	 226
700	 160
800	 131
900	 91
10000	 2395

Features with gaps  > 40 bp are deleted 
# remaining Alignments : 53062
# unique Features these remaining alignments represent: 37840
% of total features these alignments represent : 17.64 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 1590
19	 4999
29	 5773
39	 5355
49	 4298
59	 3638
69	 3035
79	 2602
89	 2755
90	 653
91	 874
92	 1044
93	 926
94	 934
95	 918
96	 957
97	 1062
98	 1097
99	 970
100	 9582

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 18389
# unique Features these remaining alignments represent: 14564
% of total features these alignments represent : 6.79 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 538
91	 592
92	 784
93	 903
94	 944
95	 1046
96	 1229
97	 1323
98	 1138
99	 3535
100	 6357

 Features less than 92 % identity are deleted. 
# remaining Alignments : 17259
# unique Features these remaining alignments represent: 13718
% of total features these alignments represent : 6.40 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 11147
2	 1976
3	 393
4	 124
5	 39
6	 19
8	 12
9	 4
10	 1
20	 3
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 16278
# unique Features these remaining alignments represent: 13516
% of total features these alignments represent : 6.30 %