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


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

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

668 Rice_unmapped_BAC_front 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 : 701
# unique Features these alignments represent: 663
% of total features these alignments represent : 99.25 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 556
1	 19
2	 7
3	 7
4	 7
5	 1
6	 1
7	 3
8	 1
9	 1
10	 0
20	 7
30	 4
40	 6
50	 2
60	 5
70	 1
80	 0
90	 2
100	 0
200	 6
300	 5
400	 3
500	 7
600	 1
700	 1
800	 0
900	 2
10000	 20

Features with gaps > 40 bp are deleted 
# remaining Alignments : 620
# unique Features these remaining alignments represent: 597
% of total features these alignments represent : 89.37 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 2
29	 1
39	 2
49	 2
59	 0
69	 3
79	 4
89	 2
90	 1
91	 0
92	 2
93	 2
94	 0
95	 1
96	 3
97	 2
98	 6
99	 14
100	 573

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 603
# unique Features these remaining alignments represent: 580
% of total features these alignments represent : 86.83 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 0
91	 0
92	 0
93	 0
94	 0
95	 0
96	 0
97	 1
98	 5
99	 84
100	 513

 Features less than 92 % identity are deleted. 
# remaining Alignments : 603
# unique Features these remaining alignments represent: 580
% of total features these alignments represent : 86.83 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 568
2	 7
3	 3
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 : 591
# unique Features these remaining alignments represent: 578
% of total features these alignments represent : 86.53 %