This reports the protocol used to align the Maize_ISU_MAGIs_3_1_w_singleton features to Maize_BACs.
 Kiran Ratnapu 
Tue May 31 16:16:53 2005


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

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

214471 Maize_ISU_MAGIs_3_1_w_singleton are aligned to Maize_BACs 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 : 68240
# unique Features these alignments represent: 26096
% of total features these alignments represent : 12.17 %

Following is the RICE_GAP distribution 
Rice_Gaps	# alignments
--------	--------
0	 24131
1	 4967
2	 2709
3	 1730
4	 1319
5	 1159
6	 1105
7	 1107
8	 916
9	 797
10	 718
20	 5022
30	 2930
40	 1828
50	 1311
60	 1027
70	 894
80	 671
90	 591
100	 509
200	 2798
300	 1198
400	 759
500	 511
600	 212
700	 170
800	 146
900	 92
10000	 2487

Features with gaps on rice > 40 bp are deleted 
# remaining Alignments : 50438
# unique Features these remaining alignments represent: 18967
% of total features these alignments represent : 8.84 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 1416
19	 4626
29	 5349
39	 5009
49	 4076
59	 3493
69	 2854
79	 2500
89	 2555
90	 625
91	 864
92	 1018
93	 933
94	 909
95	 911
96	 941
97	 1043
98	 1070
99	 938
100	 9308

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 17957
# unique Features these remaining alignments represent: 8333
% of total features these alignments represent : 3.89 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 523
91	 574
92	 782
93	 885
94	 935
95	 1035
96	 1209
97	 1297
98	 1111
99	 3428
100	 6178

 Features less than 92 % identity are deleted. 
# remaining Alignments : 16860
# unique Features these remaining alignments represent: 7635
% of total features these alignments represent : 3.56 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 5940
2	 1247
3	 283
4	 100
5	 34
6	 15
8	 10
9	 3
10	 0
20	 2
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 9283
# unique Features these remaining alignments represent: 7470
% of total features these alignments represent : 3.48 %