Schema for NSome Stringency - Nucleosome Positioning Stringency from SOLiD Core Alignments
  Database: ce6    Primary Table: nucleosomeStringency    Row Count: 96,539   Data last updated: 2008-09-29
Format description: Wiggle track values to display as y-values (first 6 fields are bed6)
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chrIvarchar(255) values Reference sequence chromosome or scaffold
chromStart 218int(10) unsigned range Start position in chromosome
chromEnd 1242int(10) unsigned range End position in chromosome
name chrI.0varchar(255) values Name of item
span 1int(10) unsigned range each value spans this many bases
count 1024int(10) unsigned range number of values in this block
offset 0int(10) unsigned range offset in File to fetch data
file /gbdb/ce6/wib/nucleosomeStr...varchar(255) values path name to data file, one byte per value
lowerLimit 0double range lowest data value in this block
dataRange 0.333333double range lowerLimit + dataRange = upperLimit
validCount 1024int(10) unsigned range number of valid data values in this block
sumData 12.6473double range sum of the data points, for average and stddev calc
sumSquares 2.59866double range sum of data points squared, for stddev calc

Sample Rows
 
binchromchromStartchromEndnamespancountoffsetfilelowerLimitdataRangevalidCountsumDatasumSquares
585chrI2181242chrI.0110240/gbdb/ce6/wib/nucleosomeStringency.wib00.333333102412.64732.59866
585chrI12422266chrI.1110241024/gbdb/ce6/wib/nucleosomeStringency.wib00.433735102444.73138.45217
585chrI22663290chrI.2110242048/gbdb/ce6/wib/nucleosomeStringency.wib00.45454510248.648842.96779
585chrI32904314chrI.3110243072/gbdb/ce6/wib/nucleosomeStringency.wib00.7102459.292212.8079
585chrI43145338chrI.4110244096/gbdb/ce6/wib/nucleosomeStringency.wib00.414286102444.76979.49176
585chrI53386362chrI.5110245120/gbdb/ce6/wib/nucleosomeStringency.wib00.428571102433.51465.14899
585chrI63627386chrI.6110246144/gbdb/ce6/wib/nucleosomeStringency.wib00.289474102442.73017.27207
585chrI73868410chrI.7110247168/gbdb/ce6/wib/nucleosomeStringency.wib00.261905102468.45298.64823
585chrI84109434chrI.8110248192/gbdb/ce6/wib/nucleosomeStringency.wib00.322581102453.08737.29867
585chrI943410458chrI.9110249216/gbdb/ce6/wib/nucleosomeStringency.wib00.333333102443.90427.47667

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

NSome Stringency (nucleosomeStringency) Track Description
 

Methods

The plot represents stringency of nucleosome positioning (at the dyad) as a fraction of positioned nucleosomes. Stringency metric is given by a ratio of putative mononucleosome dyad instances falling in a 23 base pair window of a given site to the number of infringing nucleosome dyads in a 300 base pair window.

Credits

The data for this track is supplied by the Sidow Lab and the Fire Lab at the Stanford School of Medicine.
Track display advice provided by Hiram Clawson, UCSC Genome Browser Engineering.

References

Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 2008 Jul;18(7):1051-63. PMID: 18477713; PMC: PMC2493394

Supported oligo ligation detection (SOLiD) sequencing technology from Applied Biosystems.