Schema for Gap - Gap Locations |
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Database: hg38 Primary Table: gap Row Count: 829 Data last updated: 2022-10-18
Format description: Gaps in golden path
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| 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 | 10000 | 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 | 10000 | 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 | 10000 | 1 | N | 10000 | telomere | no |
| 586 | chr1 | 207666 | 257666 | 5 | N | 50000 | contig | no |
| 587 | chr1 | 297968 | 347968 | 7 | N | 50000 | contig | no |
| 589 | chr1 | 535988 | 585988 | 10 | N | 50000 | contig | no |
| 605 | chr1 | 2702781 | 2746290 | 48 | N | 43509 | scaffold | yes |
| 85 | chr1 | 12954384 | 13004384 | 224 | N | 50000 | scaffold | yes |
| 713 | chr1 | 16799163 | 16849163 | 277 | N | 50000 | scaffold | yes |
| 810 | chr1 | 29552233 | 29553835 | 491 | N | 1602 | scaffold | yes |
| 1515 | chr1 | 121976459 | 122026459 | 1845 | N | 50000 | contig | no |
| 1517 | chr1 | 122224535 | 122224635 | 1847 | N | 100 | 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 GRCh38 (hg38) genome assembly defined in the
AGP file delivered with the sequence. These gaps are being closed during the
finishing process on the human genome. For information on the AGP file format, see the NCBI
AGP Specification. The NCBI website also provides an
overview of genome assembly procedures, as well as
specific information about the hg38 assembly.
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:
- short_arm - short arm gaps (count: 5; size range: 5,000,000 - 16,990,000 bases)
- heterochromatin - heterochromatin gaps (count: 11; size range: 20,000 - 30,000,000 bases)
- telomere - telomere gaps (count: 48; all of size 10,000 bases)
- contig - gaps between contigs in scaffolds (count: 285; size range: 100 - 400,000 bases)
- scaffold - gaps between scaffolds in chromosome assemblies (count: 470; size range: 10 - 624,000 bases)
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US Server