This reports the protocol used to align the RicePunctata_BACend_OP__B_OMAP-20070815 features to indica-genome.
Tue Aug 21 13:25:37 2007


Source of RicePunctata_BACend_OP__B_OMAP-20070815 : from Gramene markers database, originally Downloaded from genbank nucleotide databse with keyword 'OP__Ba'   

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

68384 RicePunctata_BACend_OP__B_OMAP-20070815 are aligned to indica-genome using blat with blat parameters -minIdentity=50 -minScore=10 -maxGap=3 followed by PslReps with -minNearTopSize=75 -minAli=0.25. This was followed by a filtering procedure described below and applied in general to 'OMAPSpecies-Genomic' data sets.

Initial summary
# alignments : 81930
# unique Features these alignments represent: 63561
% of total features these alignments represent : 92.95 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 3207
150	 3550
200	 4451
250	 4718
300	 5203
350	 5155
400	 5123
450	 5235
500	 5830
550	 6402
600	 6765
650	 7590
700	 7322
750	 5577
800	 3540
10000	 2262

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 67565
2000	 874
3000	 553
4000	 384
5000	 296
6000	 213
7000	 176
8000	 175
9000	 152
10000	 143
20000	 917

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 53904
2	 6031
3	 1759
4	 736
5	 457
6	 255
8	 217
9	 68
10	 33
20	 95
30	 4
40	 2
50	 0
100	 0

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 1
30	 5
40	 26
50	 90
60	 419
70	 1551
80	 7005
90	 28286
100	 44547

Following is the final summary
# alignments : 81930
# unique Features these alignments represent: 63561
% of total features these alignments represent : 92.95 %
  

Last modified: Thu Sep 13 15:01:03 2007