This reports the protocol used to align the Maize_MethylFilter_Orion features to tigrv4-genome.
Fri Apr 14 18:35:21 2006


Source of Maize_MethylFilter_Orion : Methyl-filtered TIGR maize sequence, downloaded from genbank with query '(txid4577[ORGN] AND Quackenbush[AUTH] AND "methylation"[ALL] )' 

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

450197 Maize_MethylFilter_Orion are aligned to tigrv4-genome 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 : 191785
# unique Features these alignments represent: 173418
% of total features these alignments represent : 38.52 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 43690
150	 24249
200	 23050
250	 20390
300	 17312
350	 14570
400	 12185
450	 9669
500	 7807
550	 6076
600	 4538
650	 3079
700	 2075
750	 1275
800	 776
10000	 1044

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 148589
# unique Features these remaining alignments represent: 137103
% of total features these alignments represent : 30.45 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 142713
2000	 766
3000	 262
4000	 191
5000	 231
6000	 160
7000	 156
8000	 161
9000	 97
10000	 83
20000	 635

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 143932
# unique Features these remaining alignments represent: 133287
% of total features these alignments represent : 29.61 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 127594
2	 3878
3	 691
4	 394
5	 270
6	 227
8	 143
9	 28
10	 18
20	 39
30	 2
40	 1
50	 1
100	 1

 Features that hit more than thrice are deleted. 
# remaining Alignments : 137423
# unique Features these remaining alignments represent: 132163
% of total features these alignments represent : 29.36 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 19
30	 299
40	 903
50	 1690
60	 2911
70	 9256
80	 15692
90	 73858
100	 32795

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 132013
# unique Features these remaining alignments represent: 127527
% of total features these alignments represent : 28.33 %

Following is the final summary
# alignments : 132013
# unique Features these alignments represent: 127527
% of total features these alignments represent : 28.33 %