This reports the protocol used to align the Sorghum_MethylFilter_Orion features to Maize_BACs_20060126.
Mon Feb 13 18:59:18 2006


Source of Sorghum_MethylFilter_Orion : Sorghum_Orion_Genethresher_reads, these are obtained from Orion Genomics. 

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

136197 Sorghum_MethylFilter_Orion are aligned to Maize_BACs_20060126 using blat with blat parameters -minIdentity=50 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'CrossSpecies-Genomic' data sets.

Initial summary
# alignments : 29093
# unique Features these alignments represent: 22902
% of total features these alignments represent : 16.82 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 8928
150	 3417
200	 2346
250	 1952
300	 1653
350	 1412
400	 1338
450	 1350
500	 1170
550	 994
600	 796
650	 742
700	 583
750	 417
800	 273
10000	 1722

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 20239
# unique Features these remaining alignments represent: 15798
% of total features these alignments represent : 11.60 %

Gap distribution of the remaining features
Gaps	# alignments
--------	--------
1000	 18590
2000	 460
3000	 116
4000	 65
5000	 28
6000	 25
7000	 18
8000	 45
9000	 24
10000	 33
20000	 122

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 19231
# unique Features these remaining alignments represent: 15034
% of total features these alignments represent : 11.04 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 12671
2	 1585
3	 343
4	 161
5	 126
6	 68
8	 61
9	 4
10	 2
20	 13
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 16870
# unique Features these remaining alignments represent: 14599
% of total features these alignments represent : 10.72 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 2
30	 14
40	 67
50	 291
60	 873
70	 1909
80	 2507
90	 4834
100	 6373

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 15730
# unique Features these remaining alignments represent: 13623
% of total features these alignments represent : 10.00 %

Following is the final summary
# alignments : 15730
# unique Features these alignments represent: 13623
% of total features these alignments represent : 10.00 %