Schema for Gap - Gap Locations |
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Database: mm10 Primary Table: gap Row Count: 734 Data last updated: 2021-04-09
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 | 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 |
| 756 | chr1 | 22433268 | 22466510 | 5 | N | 33242 | contig | no |
| 144 | chr1 | 75055556 | 75121556 | 7 | N | 66000 | contig | no |
| 1236 | chr1 | 85347103 | 85447103 | 9 | N | 100000 | contig | no |
| 1776 | chr1 | 156118743 | 156168743 | 11 | N | 50000 | contig | no |
| 1981 | chr1 | 182991679 | 183038090 | 13 | N | 46411 | contig | no |
| 30 | chr1 | 183453931 | 183503931 | 15 | N | 50000 | contig | no |
| 256 | chr1 | 192001776 | 192051776 | 17 | 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 depicts gaps in the assembly
(Dec. 2011, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2))
of the mouse genome. These gaps - with the
exception of intractable centromere gaps - will be closed during the
finishing process.
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 known, 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:
(In this context, a contig is a set of overlapping sequence reads.)
- Clone - gaps between clones (114 gaps).
- Contig - gaps between map contigs, various sizes (104 gaps).
- Telomere - 42 gaps for telomeres (100,000 Ns)
- Centromere - 20 gaps for centromeres (size: 2,890,000 Ns)
- Short_arm - 21 gaps for the short arm (10,000 Ns)
at base positions 100,001-110,000 of each chromosome.
- other - sequence of Ns in the assembly that were not
marked as gaps in the AGP assembly definition file, various sizes (384 gaps).
- Fragment - a single gap of 31 bases in chrX_GL456233_random.
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