This reports the protocol used to align the Rice_unmapped_BAC_back features to tigrv4-genome.
Fri Apr 14 11:55:22 2006


Source of Rice_unmapped_BAC_back : Downloaded from NCBI Genbank, Rice BACs or clones not used on the assembly  

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

668 Rice_unmapped_BAC_back are aligned to tigrv4-genome 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 : 682
# unique Features these alignments represent: 665
% of total features these alignments represent : 99.55 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 561
1	 13
2	 11
3	 4
4	 4
5	 2
6	 2
7	 0
8	 1
9	 1
10	 1
20	 6
30	 3
40	 6
50	 4
60	 2
70	 1
80	 1
90	 4
100	 0
200	 7
300	 7
400	 3
500	 5
600	 1
700	 1
800	 0
900	 1
10000	 18

Features with gaps > 40 bp are deleted 
# remaining Alignments : 615
# unique Features these remaining alignments represent: 601
% of total features these alignments represent : 89.97 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 1
29	 0
39	 3
49	 2
59	 0
69	 3
79	 0
89	 5
90	 0
91	 0
92	 1
93	 1
94	 2
95	 0
96	 0
97	 2
98	 4
99	 20
100	 571

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 601
# unique Features these remaining alignments represent: 588
% of total features these alignments represent : 88.02 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 0
95	 0
96	 0
97	 4
98	 5
99	 86
100	 506

 Features less than 92 % identity are deleted. 
# remaining Alignments : 601
# unique Features these remaining alignments represent: 588
% of total features these alignments represent : 88.02 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 582
2	 4
3	 0
4	 1
5	 0
6	 0
8	 1
9	 0
10	 0
20	 0
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted.  
# remaining Alignments : 590
# unique Features these remaining alignments represent: 586
% of total features these alignments represent : 87.72 %