Schema for Quality Scores - Cow Sequencing Quality Scores

Schema for Quality Scores - Cow Sequencing Quality Scores

Database: bosTau4 Primary Table: quality Row Count: 2,855,674
Format description: Wiggle track values to display as y-values (first 6 fields are bed6)

field	example	SQL type	description
`bin`	585	`smallint unsigned`	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	Reference sequence chromosome or scaffold
`chromStart`	0	`int unsigned`	Start position in chromosome
`chromEnd`	1024	`int unsigned`	End position in chromosome
`name`	chr1.86443	`varchar(255)`	Name of item
`span`	1	`int unsigned`	each value spans this many bases
`count`	1024	`int unsigned`	number of values in this block
`offset`	88516663	`int unsigned`	offset in File to fetch data
`file`	/gbdb/bosTau4/wib/qual.wib	`varchar(255)`	path name to data file, one byte per value
`lowerLimit`	0	`double`	lowest data value in this block
`dataRange`	62	`double`	lowerLimit + dataRange = upperLimit
`validCount`	1024	`int unsigned`	number of valid data values in this block
`sumData`	39136	`double`	sum of the data points, for average and stddev calc
`sumSquares`	1808900	`double`	sum of data points squared, for stddev calc

Sample Rows

bin	chrom	chromStart	chromEnd	name	span	count	offset	file	lowerLimit	dataRange	validCount	sumData	sumSquares
585	chr1	0	1024	chr1.86443	1	1024	88516663	/gbdb/bosTau4/wib/qual.wib	0	62	1024	39136	1808900
585	chr1	1024	2048	chr1.86444	1	1024	88517687	/gbdb/bosTau4/wib/qual.wib	39	51	1024	70617	5098200
585	chr1	2048	3072	chr1.86445	1	1024	88518711	/gbdb/bosTau4/wib/qual.wib	10	80	1024	67692	4581910
585	chr1	3072	4096	chr1.86446	1	1024	88519735	/gbdb/bosTau4/wib/qual.wib	0	72	1024	29557	1760820
585	chr1	4096	5120	chr1.86447	1	1024	88520759	/gbdb/bosTau4/wib/qual.wib	54	18	1024	72948	5200370
585	chr1	5120	6144	chr1.86448	1	1024	88521783	/gbdb/bosTau4/wib/qual.wib	56	16	1024	71786	5039920
585	chr1	6144	7168	chr1.86449	1	1024	88522807	/gbdb/bosTau4/wib/qual.wib	57	33	1024	87044	7472890
585	chr1	7168	8192	chr1.86450	1	1024	88523831	/gbdb/bosTau4/wib/qual.wib	90	0	1024	92160	8294400
585	chr1	8192	9216	chr1.86451	1	1024	88524855	/gbdb/bosTau4/wib/qual.wib	64	26	1024	91416	8173420
585	chr1	9216	10240	chr1.86452	1	1024	88525879	/gbdb/bosTau4/wib/qual.wib	90	0	1024	92160	8294400

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Quality Scores (quality) Track Description

Description

The Quality Scores track shows the sequencing quality score (range: 0 to 99) of each base in the assembly. The height at each position of the track indicates the quality of the base. When zoomed out to a large range, the heights reflect the averaged scores. Scores of 40 or higher reflect high confidence in the sequence (with an error rate of less than 1/10,000); scores of 20 or higher reflect reasonable confidence (of working draft quality).

This track may be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Credits

The quality scores were provided as part of the cow assembly. The database representation and graphical display code were written by Hiram Clawson.