This reports the protocol used to align the RiceGlaberrima_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 12:17:23 2006


Source of RiceGlaberrima_BACend_OMAP : from Gramene markers database, originally Downloaded from genbank nucleotide databse with keyword 'OG_BBa'   

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

67158 RiceGlaberrima_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 : 97161
# unique Features these alignments represent: 62944
% of total features these alignments represent : 93.73 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 52347
1	 11019
2	 5052
3	 3351
4	 2242
5	 1766
6	 1540
7	 1204
8	 901
9	 1005
10	 743
20	 3895
30	 1907
40	 1012
50	 639
60	 419
70	 301
80	 283
90	 175
100	 190
200	 998
300	 688
400	 505
500	 391
600	 88
700	 61
800	 71
900	 48
10000	 1190

Features with gaps > 40 bp are deleted 
# remaining Alignments : 87984
# unique Features these remaining alignments represent: 57118
% of total features these alignments represent : 85.05 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 0
19	 0
29	 73
39	 197
49	 306
59	 518
69	 577
79	 769
89	 2154
90	 600
91	 892
92	 1121
93	 1522
94	 2523
95	 3984
96	 6422
97	 9763
98	 14156
99	 18877
100	 23530

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 82804
# unique Features these remaining alignments represent: 53070
% of total features these alignments represent : 79.02 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 139
91	 223
92	 406
93	 983
94	 1881
95	 3902
96	 7295
97	 13459
98	 20827
99	 28839
100	 4850

 Features less than 92 % identity are deleted. 
# remaining Alignments : 82442
# unique Features these remaining alignments represent: 52847
% of total features these alignments represent : 78.69 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 46322
2	 2053
3	 1181
4	 858
5	 595
6	 354
8	 865
9	 97
10	 104
20	 268
30	 45
40	 29
50	 15
100	 50

 Features that hit more than thrice are deleted.  
# remaining Alignments : 53971
# unique Features these remaining alignments represent: 49556
% of total features these alignments represent : 73.79 %