This reports the protocol used to align the Maize_FSTMu features to tigrv4-genome.
Fri Apr 14 16:28:33 2006


Source of Maize_FSTMu : Downloaded from genbank with query ' (txid4577[ORGN] AND Walbot[AUTH] AND RescueMu[TITL])' 

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

178124 Maize_FSTMu 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 : 62399
# unique Features these alignments represent: 50910
% of total features these alignments represent : 28.58 %

The length of the matches are distributed as follows 
Hit_length	# alignments
--------	--------
100	 23197
150	 13403
200	 10804
250	 5133
300	 5740
350	 1534
400	 1122
450	 583
500	 458
550	 266
600	 101
650	 54
700	 4
750	 0
800	 0
10000	 0

Alignments with matches less than 100 bp are filtered 
# remaining Alignments : 39379
# unique Features these remaining alignments represent: 31427
% of total features these alignments represent : 17.64 %

gap distribution of the remaining features
gaps	# alignments
--------	--------
1000	 39146
2000	 3
3000	 3
4000	 23
5000	 35
6000	 5
7000	 8
8000	 1
9000	 2
10000	 2
20000	 23

Alignments with gaps  > 4000 bp are filtered
# remaining Alignments : 39175
# unique Features these remaining alignments represent: 31261
% of total features these alignments represent : 17.55 %

Frequency distribution of the remaining features
# hits	# features
--------	--------
1	 29297
2	 644
3	 214
4	 234
5	 294
6	 125
8	 93
9	 45
10	 28
20	 287
30	 0
40	 0
50	 0
100	 0

 Features that hit more than thrice are deleted. 
# remaining Alignments : 31227
# unique Features these remaining alignments represent: 30155
% of total features these alignments represent : 16.93 %

% Identity distribution of the remaining features
% Identity	# alignemnts
--------	--------
10	 0
20	 0
30	 8
40	 11
50	 39
60	 84
70	 301
80	 3754
90	 17191
100	 9839

 Alignments with percent identity lower than 60 deleted. 
# remaining Alignments : 31092
# unique Features these remaining alignments represent: 30035
% of total features these alignments represent : 16.86 %

Following is the final summary
# alignments : 31092
# unique Features these alignments represent: 30035
% of total features these alignments represent : 16.86 %