Schema for Gap - Gap Locations
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Database: mm39 Primary Table: gap Row Count: 324   Data last updated: 2020-07-27
Format description: Gaps in golden path On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 585 | smallint(6) | range | Indexing field to speed chromosome range queries. |
chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
chromStart | 0 | int(10) unsigned | range | start position in chromosome |
chromEnd | 100000 | int(10) unsigned | range | end position in chromosome |
ix | 1 | int(11) | range | index count of this fragment (obsolete/useless) |
n | N | char(1) | values | 'N' for gaps of known size, 'U' for gaps of unknown size |
size | 100000 | int(10) unsigned | range | size of gap |
type | telomere | varchar(255) | values | scaffold, contig, clone, fragment, etc. |
bridge | no | varchar(255) | values | yes, no, mrna, bacEndPair, etc. |
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Sample Rows
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bin | chrom | chromStart | chromEnd | ix | n | size | type | bridge |
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585 | chr1 | 0 | 100000 | 1 | N | 100000 | telomere | no |
585 | chr1 | 100000 | 110000 | 2 | N | 10000 | short_arm | no |
9 | chr1 | 110000 | 3000000 | 3 | N | 2890000 | centromere | no |
75 | chr1 | 3000000 | 3050000 | 4 | N | 50000 | contig | no |
154 | chr1 | 85324824 | 85374824 | 677 | N | 50000 | contig | no |
2073 | chr1 | 195054279 | 195154279 | 1586 | N | 100000 | telomere | no |
585 | chr10 | 0 | 100000 | 1 | N | 100000 | telomere | no |
585 | chr10 | 100000 | 110000 | 2 | N | 10000 | short_arm | no |
9 | chr10 | 110000 | 3000000 | 3 | N | 2890000 | centromere | no |
75 | chr10 | 3000000 | 3050000 | 4 | N | 50000 | contig | no |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Gap (gap) Track Description
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Description
This track shows the gaps in the Jun. 2020 mouse 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 contains the following principal types of gaps:
- centromere - gaps for centromeres are included when they can be reasonably localized (count: 20; all of size 2,890,000 bases)
- short_arm - a gap inserted at the start of an acrocentric chromosome (count: 21; all of size 10,000 bases)
- telomere - telomere gaps (count: 42; all of size 100,000 bases)
- contig - gaps between contigs in scaffolds (count: 60; size range: 8,000 - 500,000 bases)
- scaffold - gaps between scaffolds in chromosome assemblies (count: 181; size range: 27 - 522,000 bases)
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