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Schema for Gap - Gap Locations |
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Database: bosTau4 Primary Table: gap Row Count: 75,654
Format description: Gaps in golden path
| field | example | SQL type | info | description |
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| bin | 585 | smallint | range | Indexing field to speed chromosome range queries. |
| chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
| chromStart | 3267 | int unsigned | range | start position in chromosome |
| chromEnd | 3767 | int unsigned | range | end position in chromosome |
| ix | 2 | int | range | ix of this fragment (useless) |
| n | N | char(1) | values | always 'N' |
| size | 500 | int unsigned | range | size of gap |
| type | fragment | varchar(255) | values | contig, clone, fragment, etc. |
| bridge | yes | varchar(255) | values | yes, no, mrna, bacEndPair, etc. |
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| bin | chrom | chromStart | chromEnd | ix | n | size | type | bridge |
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| 585 | chr1 | 3267 | 3767 | 2 | N | 500 | fragment | yes |
| 586 | chr1 | 179663 | 179713 | 8 | N | 50 | fragment | yes |
| 586 | chr1 | 194311 | 194640 | 10 | N | 329 | fragment | yes |
| 586 | chr1 | 195970 | 196020 | 12 | N | 50 | fragment | yes |
| 587 | chr1 | 296356 | 296610 | 15 | N | 254 | fragment | yes |
| 587 | chr1 | 324053 | 324103 | 18 | N | 50 | fragment | yes |
| 589 | chr1 | 564167 | 569167 | 23 | N | 5000 | clone | no |
| 589 | chr1 | 572233 | 572283 | 25 | N | 50 | fragment | yes |
| 591 | chr1 | 837725 | 838408 | 28 | N | 683 | fragment | yes |
| 591 | chr1 | 843892 | 844548 | 31 | N | 656 | fragment | yes |
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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.
Many of these gaps — with the
exception of intractable heterochromatic gaps — may 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 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:
- Fragment - gaps between the Whole Genome Shotgun contigs of a
supercontig. (In this context, a contig is a set of overlapping sequence reads.
A supercontig is a set of contigs ordered and oriented during the
Whole Genome Shotgun process using paired-end reads.)
These are represented by varying numbers of Ns in the assembly.
Fragment gap sizes are usually taken from read pair data.
- Clone - gaps between supercontigs linked by the fingerprint map.
In general, these are represented by 5,000 Ns in the assembly.
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