This reports the protocol used to align the Maize_HiCotMethylFilterCluster_TIGR features to tigrv4-genome.
Fri Apr 14 18:18:46 2006


Source of Maize_HiCotMethylFilterCluster_TIGR : from Gramene markers database, originally Downloaded from TIGR using the link ftp://ftp.tigr.org/pub/data/MAIZE/AZMs/release_4.0/zmg_fasta.4.0ALL_022304.gz 

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

243807 Maize_HiCotMethylFilterCluster_TIGR 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 : 102676
# unique Features these alignments represent: 86409
% of total features these alignments represent : 35.44 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 31740
150	 11003
200	 9278
250	 7543
300	 6329
350	 5352
400	 4680
450	 4134
500	 3609
550	 2909
600	 2500
650	 2039
700	 1710
750	 1502
800	 1461
10000	 6887

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 71229
# unique Features these remaining alignments represent: 61442
% of total features these alignments represent : 25.20 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 62023
2000	 3445
3000	 1111
4000	 569
5000	 295
6000	 144
7000	 124
8000	 117
9000	 82
10000	 55
20000	 461

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 67148
# unique Features these remaining alignments represent: 58030
% of total features these alignments represent : 23.80 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 53650
2	 2699
3	 593
4	 379
5	 293
6	 199
8	 120
9	 22
10	 30
20	 39
30	 1
40	 2
50	 2
100	 1

 Features that hit more than thrice are deleted. 
# remaining Alignments : 60827
# unique Features these remaining alignments represent: 56942
% of total features these alignments represent : 23.36 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 16
30	 277
40	 925
50	 1767
60	 2850
70	 7573
80	 8364
90	 29605
100	 9450

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 55360
# unique Features these remaining alignments represent: 52151
% of total features these alignments represent : 21.39 %

Following is the final summary
# alignments : 55360
# unique Features these alignments represent: 52151
% of total features these alignments represent : 21.39 %