stat.out

stat.out

The stat.out file contains information about the number of the found differences between the query and reference sequences.

The following information is provided in the file:

• The total number of all reshufflings, inversions, wrong sequences and all types of insertions, deletions, substitutions, translocations, and relocations (Total number).
• The number of all insertions, deletions, substitutions, translocations, and relocations separately for each group.
• The total number of reshufflings, reshuffled fragments (reshuffled blocks), inversions, and wrong sequences.
• The number of reference regions that were not covered by any query sequence (Uncovered ref regions num) and the total length of these regions (Uncovered ref regions len)
• A detailed information about the number of insertions, deletions, substitutions, relocations and translocations separately for each type.

As an additional information, the number of sequences in query and reference genomes is provided.

An example of the stat.out file:

Total number	800
Insertions	143
Deletions	91
Substitutions	525
Translocations	0
Relocations	26
Reshufflings	4
Reshuffled blocks	14
Inversions	10
Unaligned sequences	0

Uncovered ref regions num	13
Uncovered ref regions len	45120

DETAILED INFORMATION:	
substitution	483
gap	42

insertion	73
duplication	5
tandem_duplication	0
unaligned_beginning	0
unaligned_end	2
inserted_gap	63

deletion	77
collapsed_repeat	9
tandem_collapsed_repeat	5

translocation	0
translocation-insertion	0
translocation-insertion_ATGCN	0
translocation-inserted_gap	0
translocation-overlap	0

circular_genome_start	1
relocation	1
relocation-insertion	1
relocation-insertion_ATGCN	1
relocation-inserted_gap	9
relocation-overlap	14


ADDITIONAL INFORMATION:
query sequences 10
reference sequences 2