MaizeGDB is a community-oriented, long-term, federally funded
informatics service to researchers focused on the crop plant and
model organism Zea mays.
MaizeGDB is a founding member of
AgBioData,
a consortuim of agriculture-related online resources which is
committed to making agriculture-related research data FAIR.
GCV: A web-app that visualizes genomic context data in a single, federated interface by using functional annotations as a unit of search and comparison.
Ying Hu, Vincent Colantonio, Bárbara S. F. Müller, Kristen Leach, Adalena Nanni, Christina Finegan, Bo Wang, Matheus Baseggio , Lily Hislop, Kelly Swarts, Michael A. Gore, Tracie A. Bierwagen, Alan Myers, A. Mark Settles, William F. Tracy
Funding
SweetCAP - USDA NIFA - 2018-51181-28419
Publication status
Published
Project reference
Chromosome-scale genome assembly and population genomic analysis provides insights into the origin and evolution of modern sweet corn.
Ying Hu, Vincent Colantonio, Bárbara S F Müller, Kristen A Leach, Adalena Nanni, Christina Finegan, Bo Wang, Matheus Baseggio, Carter J Newton, Emily M Juhl, Lillian Hislop, Juan M Gonzalez, Esteban F Rios, L Curtis Hannah, Kelly Swarts, Michael A Gore, Tracie A Hennen-Bierwagen, Alan M Myers, A Mark Settles, William F Tracy, Marcio F R Resende Jr
PMID DOI
Stock and Biosample Information
Stock information
Stock name
We are currently in the process of submitting it to USDA GRIN
Stock details
We are currently in the process of submitting it to USDA GRIN
Stock provided by
Marcio Resende
Biosample information
Species
Zea mays ssp. mays (maize)
Sample name
Ia453-sh2
Sample description
This is a sweet corn inbred line, Ia453, with the mutated shrunken2-Reference allele.
The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 50% of the total assembly size.
How many scaffolds are counted in reaching the N50 threshold.
The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 90% of the total assembly size.
How many scaffolds are counted in reaching the N90 threshold.
Total sequence length represented by contigs.
The longest contig.
The shortest contig.
The length of contig which takes the sum length (summing from longest to shortest contig) past 50% of the total assembly size.
How many contig are counted in reaching the N50 threshold.
The length of contig which takes the sum length (summing from longest to shortest contig) past 90% of the total assembly size.
How many contig are counted in reaching the N90 threshold.
A contig is a contiguous consensus sequence that is
derived from a collection of overlapping reads.
A scaffold is set of a ordered and orientated contigs
that are linked to one another by mate pairs of sequencing reads.
Annotation
Annotation Identifier
Zm00045a.1
Annotation Provider
Marcio Resende
Annotation Date
2019.08
Is current
yes
Annotation Software
MAKER-P v2.31.10
Annotation Description
MAKER-P v2.31.10 was used to annotate genes in the Ia453-sh2 genome with the evidence data from the annotation of the B73v4 genome and including some new evidence.
