This reports the protocol used to align the Maize_HiCot_Bennetzen features to Maize_BACs_20060126.
Mon Feb 13 23:16:16 2006


Source of Maize_HiCot_Bennetzen : Downloaded from Genbank with query '(txid4577[ORGN] AND Bennetzen[AUTH] AND Cot[ALL])' 

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

446926 Maize_HiCot_Bennetzen 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 : 106493
# unique Features these alignments represent: 74234
% of total features these alignments represent : 16.61 %

Following is the Gap distribution 
Gaps	# alignments
--------	--------
0	 37759
1	 13688
2	 5895
3	 3340
4	 2255
5	 1887
6	 1668
7	 1615
8	 1311
9	 1145
10	 1066
20	 7241
30	 3923
40	 2421
50	 1810
60	 1440
70	 1088
80	 851
90	 698
100	 675
200	 3811
300	 1545
400	 1095
500	 617
600	 231
700	 194
800	 132
900	 110
10000	 2511

Features with gaps  > 40 bp are deleted 
# remaining Alignments : 85214
# unique Features these remaining alignments represent: 58995
% of total features these alignments represent : 13.20 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 426
29	 9497
39	 9151
49	 5803
59	 4268
69	 3559
79	 2748
89	 3710
90	 784
91	 1028
92	 1131
93	 1425
94	 1705
95	 1987
96	 2644
97	 3171
98	 3752
99	 4657
100	 23768

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 45281
# unique Features these remaining alignments represent: 30571
% of total features these alignments represent : 6.84 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 409
91	 527
92	 888
93	 1407
94	 1777
95	 2452
96	 3332
97	 4068
98	 4383
99	 16136
100	 9902

 Features less than 92 % identity are deleted. 
# remaining Alignments : 44345
# unique Features these remaining alignments represent: 29936
% of total features these alignments represent : 6.70 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 23133
2	 4419
3	 1048
4	 417
5	 268
6	 211
8	 186
9	 56
10	 45
20	 132
30	 8
40	 6
50	 2
100	 5

 Features that hit more than thrice are deleted.  
# remaining Alignments : 35115
# unique Features these remaining alignments represent: 28600
% of total features these alignments represent : 6.40 %