Schema for Hg19 Diff - Contigs New to GRCh38/(hg38), Not Carried Forward from GRCh37/(hg19) |
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Database: hg38 Primary Table: hg38ContigDiff Row Count: 23,632 Data last updated: 2014-01-01
Format description: Browser extensible data
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| bin | 586 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
| chromStart | 177417 | int(10) unsigned | range | Start position in chromosome |
| chromEnd | 207666 | int(10) unsigned | range | End position in chromosome |
| name | FO538757.3 | varchar(255) | values | Name of item |
| score | 0 | int(10) unsigned | range | Optional score, nominal range 0-1000 |
| strand | + | char(1) | values | + or - |
| thickStart | 177417 | int(10) unsigned | range | Start of where display should be thick (start codon) |
| thickEnd | 207666 | int(10) unsigned | range | End of where display should be thick (stop codon) |
| itemRgb | 14163461 | 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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hg38.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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| 586 | chr1 | 177417 | 207666 | FO538757.3 | 0 | + | 177417 | 207666 | 216,30,5 |
| 73 | chr1 | 347968 | 501617 | AL732372.15 | 500 | - | 347968 | 501617 | 163,130,5 |
| 73 | chr1 | 501617 | 535988 | FO681485.2 | 0 | - | 501617 | 535988 | 216,30,5 |
| 73 | chr1 | 697537 | 835050 | AL669831.13 | 500 | + | 697537 | 835050 | 163,130,5 |
| 591 | chr1 | 835050 | 835333 | KF495845.1 | 0 | - | 835050 | 835333 | 216,30,5 |
| 591 | chr1 | 835333 | 871977 | AL669831.13 | 500 | + | 835333 | 871977 | 163,130,5 |
| 591 | chr1 | 871977 | 872551 | KF454898.1 | 0 | + | 871977 | 872551 | 216,30,5 |
| 591 | chr1 | 872551 | 877104 | AL669831.13 | 500 | + | 872551 | 877104 | 163,130,5 |
| 594 | chr1 | 1191888 | 1261208 | AL162741.44 | 500 | + | 1191888 | 1261208 | 163,130,5 |
| 594 | chr1 | 1261208 | 1261666 | KF495840.1 | 0 | - | 1261208 | 1261666 | 216,30,5 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Hg19 Diff (hg38ContigDiff) Track Description
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Description
This track shows the differences between the GRCh38 (hg38) and previous GRCh37 (hg19)
human genome assemblies, indicating contigs (or portions of contigs) that are new
to the hg38 assembly.
The following color/score key is used:
| color | score | change from hg19 to hg38 |
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| | 0 | New contig added to
hg38 to update sequence or fill gaps present in hg19 |
| | 500 | Different portions
of this same contig used in the construction of hg38 and hg19 assemblies |
| | 1000 | Updated version of
an hg19 contig in which sequence errors have been corrected |
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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US Server