This reports the protocol used to align the RiceNivara_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 16:21:06 2006


Source of RiceNivara_BACend_OMAP : from Gramene markers database, originally From genbank Nucleotide database with keyword 'OR_BBa'  

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

106124 RiceNivara_BACend_OMAP 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 : 233996
# unique Features these alignments represent: 102172
% of total features these alignments represent : 96.28 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 131361
1	 30102
2	 11079
3	 6620
4	 4453
5	 3361
6	 3200
7	 2318
8	 1731
9	 1495
10	 1490
20	 6768
30	 3242
40	 1696
50	 1252
60	 897
70	 719
80	 561
90	 308
100	 315
200	 2696
300	 1270
400	 904
500	 670
600	 249
700	 177
800	 291
900	 137
10000	 3270

Features with gaps > 40 bp are deleted 
# remaining Alignments : 208916
# unique Features these remaining alignments represent: 92267
% of total features these alignments represent : 86.94 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 0
29	 103
39	 304
49	 284
59	 607
69	 836
79	 1066
89	 2916
90	 860
91	 1174
92	 1600
93	 2348
94	 3630
95	 6204
96	 11921
97	 22087
98	 33159
99	 54988
100	 64829

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 201952
# unique Features these remaining alignments represent: 87742
% of total features these alignments represent : 82.68 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 135
91	 324
92	 647
93	 1374
94	 3204
95	 7840
96	 18060
97	 28472
98	 54071
99	 79247
100	 8578

 Features less than 92 % identity are deleted. 
# remaining Alignments : 201493
# unique Features these remaining alignments represent: 87521
% of total features these alignments represent : 82.47 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 71370
2	 3641
3	 2404
4	 2026
5	 1423
6	 900
8	 2260
9	 428
10	 411
20	 1484
30	 491
40	 328
50	 127
100	 161

 Features that hit more than thrice are deleted.  
# remaining Alignments : 85864
# unique Features these remaining alignments represent: 77415
% of total features these alignments represent : 72.95 %