This reports the protocol used to align the RiceJaponica_BACend_OMAP features to tigrv4-genome.
Fri Apr 14 18:41:55 2006


Source of RiceJaponica_BACend_OMAP : from Gramene markers database, originally Downloaded from genbank using the query '(CUGI Rice BAC end) AND (oryza [ORGN])' and only high quality sequence is extracted based on the information from genbank records   

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

249729 RiceJaponica_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 : 368234
# unique Features these alignments represent: 237528
% of total features these alignments represent : 95.11 %

Following is the GAP distribution 
Gaps	# alignments
--------	--------
0	 149271
1	 35331
2	 18811
3	 11414
4	 8743
5	 7018
6	 6972
7	 6063
8	 5766
9	 4979
10	 4788
20	 26737
30	 11710
40	 7412
50	 4913
60	 3411
70	 2454
80	 1984
90	 1628
100	 1571
200	 6370
300	 3433
400	 3215
500	 2223
600	 1419
700	 1098
800	 1065
900	 913
10000	 13661

Features with gaps > 40 bp are deleted 
# remaining Alignments : 305015
# unique Features these remaining alignments represent: 195755
% of total features these alignments represent : 78.39 %

 Following is the distribution of by feature coverage 
%coverage	# alignments
--------	--------
9	 12
19	 260
29	 4500
39	 8513
49	 13671
59	 22133
69	 34065
79	 37322
89	 43468
90	 4965
91	 5882
92	 6879
93	 7315
94	 9018
95	 7488
96	 6847
97	 7220
98	 9960
99	 16734
100	 58763

 Features less than 90 % coverage are deleted. 
# remaining Alignments : 136211
# unique Features these remaining alignments represent: 96302
% of total features these alignments represent : 38.56 %

% Identity distribution of the remaining features
% Identity	# alignments
--------	--------
90	 67
91	 100
92	 131
93	 266
94	 567
95	 1261
96	 3073
97	 8067
98	 22494
99	 55547
100	 44638

 Features less than 92 % identity are deleted. 
# remaining Alignments : 136044
# unique Features these remaining alignments represent: 96185
% of total features these alignments represent : 38.52 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 90100
2	 2249
3	 998
4	 587
5	 720
6	 276
8	 401
9	 80
10	 109
20	 313
30	 101
40	 75
50	 46
100	 75

 Features that hit more than thrice are deleted.  
# remaining Alignments : 97592
# unique Features these remaining alignments represent: 93347
% of total features these alignments represent : 37.38 %