Schema for Hg38 Diff - Contigs Dropped or Changed from GRCh37(hg19) to GRCh38(hg38) |
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Database: hg19 Primary Table: hg38ContigDiff Row Count: 6,097 Data last updated: 2014-02-13
Format description: Browser extensible data
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| bin | 73 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
| chromStart | 317719 | int(10) unsigned | range | Start position in chromosome |
| chromEnd | 471368 | int(10) unsigned | range | End position in chromosome |
| name | AL732372.15 | varchar(255) | values | Name of item |
| score | 500 | int(10) unsigned | range | Optional score, nominal range 0-1000 |
| strand | + | char(1) | values | + or - |
| thickStart | 317719 | int(10) unsigned | range | Start of where display should be thick (start codon) |
| thickEnd | 471368 | int(10) unsigned | range | End of where display should be thick (stop codon) |
| itemRgb | 10715653 | int(10) unsigned | range | Used as itemRgb as of 2004-11-22 |
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Connected Tables and Joining Fields
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hg19.gold.frag (via hg38ContigDiff.name)
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Sample Rows
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| bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | itemRgb |
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| 73 | chr1 | 317719 | 471368 | AL732372.15 | 500 | + | 317719 | 471368 | 163,130,5 |
| 73 | chr1 | 632917 | 812484 | AL669831.13 | 500 | + | 632917 | 812484 | 163,130,5 |
| 74 | chr1 | 1127268 | 1237427 | AL162741.44 | 500 | + | 1127268 | 1237427 | 163,130,5 |
| 74 | chr1 | 1237427 | 1319872 | AL139287.24 | 500 | + | 1237427 | 1319872 | 163,130,5 |
| 595 | chr1 | 1326528 | 1392451 | AL391244.11 | 500 | - | 1326528 | 1392451 | 163,130,5 |
| 74 | chr1 | 1516550 | 1621653 | AL691432.54 | 500 | + | 1516550 | 1621653 | 163,130,5 |
| 74 | chr1 | 1730263 | 1893454 | AL109917.22 | 500 | + | 1730263 | 1893454 | 163,130,5 |
| 75 | chr1 | 2684220 | 2804248 | AL592464.24 | 500 | + | 2684220 | 2804248 | 163,130,5 |
| 75 | chr1 | 2804248 | 2909351 | AL589702.8 | 500 | + | 2804248 | 2909351 | 163,130,5 |
| 76 | chr1 | 3226660 | 3365232 | AL354743.33 | 500 | + | 3226660 | 3365232 | 163,130,5 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Hg38 Diff (hg38ContigDiff) Track Description
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Description
This track shows the differences between the GRCh37 (hg19) and GRCh38 (hg38) human genome
assemblies, indicating hg19 contigs (or portions of contigs) that were not carried forward to the
newer assembly.
The following color/score key is used:
item
color | item
score | type of change from hg19 to hg38 |
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| | 0 | hg19 contig dropped in
the construction of the hg38 assembly |
| | 500 | Different portions
of this same contig used in the construction of hg38 and hg19 assemblies |
| | 1000 | Contig updated in hg38 to
correct sequence errors present in hg19 version |
Use the score filter to select which categories to show in the display.
Methods
The contig coordinates were extracted from the AGP files for both assemblies.
Contigs that matched the same name, same version, and the same specific
portion of sequence in both assemblies were considered identical between the two
assemblies and were excluded from this data set. The remaining contigs are shown
in this track.
Credits
The data and presentation of this track were prepared by
Hiram Clawson, UCSC Genome
Browser engineering.
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