Schema for Gap - Gap Locations
  Database: wuhCor1    Primary Table: gap    Row Count: 0   Data last updated: 2020-01-29
Format description: Gaps in golden path
On download server: MariaDB table dump directory
fieldSQL type info description
bin smallint(6) range Indexing field to speed chromosome range queries.
chrom varchar(255) values Reference sequence chromosome or scaffold
chromStart int(10) unsigned range start position in chromosome
chromEnd int(10) unsigned range end position in chromosome
ix int(11) range index count of this fragment (obsolete/useless)
n char(1) values 'N' for gaps of known size, 'U' for gaps of unknown size
size int(10) unsigned range size of gap
type varchar(255) values scaffold, contig, clone, fragment, etc.
bridge varchar(255) values yes, no, mrna, bacEndPair, etc.

Sample Rows

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Gap (gap) Track Description


This track shows the gaps in the Jan. 2020 sars-cov-2 genome assembly.

Genome assembly procedures are covered in the NCBI assembly documentation.
NCBI also provides specific information about this assembly.

The definition of the gaps in this assembly is from the AGP file delivered with the sequence. The NCBI document AGP Specification describes the format of the AGP file.

Gaps are represented as black boxes in this track. If the relative order and orientation of the contigs on either side of the gap is supported by read pair data, it is a bridged gap and a white line is drawn through the black box representing the gap.

This assembly has no annotated gaps.