This reports the protocol used to align the Maize_FSTMu features to Maize_BACs_20060126.
Mon Feb 13 23:46:08 2006


Source of Maize_FSTMu : Downloaded from genbank with query ' (txid4577[ORGN] AND Walbot[AUTH] AND RescueMu[TITL])' 

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

178124 Maize_FSTMu 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 : 69814
# unique Features these alignments represent: 29628
% of total features these alignments represent : 16.63 %

Following is the Gap distribution 
Gaps	# alignments
--------	--------
0	 40768
1	 5799
2	 2035
3	 1079
4	 999
5	 587
6	 713
7	 548
8	 760
9	 372
10	 414
20	 5053
30	 1623
40	 720
50	 402
60	 313
70	 127
80	 107
90	 66
100	 88
200	 4945
300	 272
400	 270
500	 223
600	 30
700	 22
800	 14
900	 10
10000	 395

Features with gaps  > 40 bp are deleted 
# remaining Alignments : 61470
# unique Features these remaining alignments represent: 23670
% of total features these alignments represent : 13.29 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 0
29	 73
39	 6010
49	 5007
59	 4024
69	 2425
79	 2266
89	 3481
90	 684
91	 859
92	 1059
93	 1253
94	 1595
95	 2264
96	 3483
97	 4591
98	 6017
99	 6973
100	 9406

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 37554
# unique Features these remaining alignments represent: 12894
% of total features these alignments represent : 7.24 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 233
91	 381
92	 591
93	 985
94	 1767
95	 2737
96	 3930
97	 6366
98	 8562
99	 4111
100	 7891

 Features less than 92 % identity are deleted. 
# remaining Alignments : 36940
# unique Features these remaining alignments represent: 12571
% of total features these alignments represent : 7.06 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 7409
2	 2855
3	 620
4	 415
5	 268
6	 203
8	 236
9	 70
10	 46
20	 234
30	 81
40	 49
50	 17
100	 46

 Features that hit more than thrice are deleted.  
# remaining Alignments : 14979
# unique Features these remaining alignments represent: 10884
% of total features these alignments represent : 6.11 %