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.
Information about assembly Zm-B104-DRAFT-ISU_USDA-0.1
(also known as B104)
Assembly identifier: Zm00007a
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Genome Sequencing Project Information
This sequence has been released under the
Toronto Agreement.
No whole-genome or whole-annotation research
may be submitted for publication until the official publication for this genome
assembly and/or annotation has been published.
Project name
Sequencing, Assembly and Annotation of B104 , A Maize Transformation Resource.
B104 seed was ordered from CAD (http://www.cad.iastate.edu/) at Iowa State Univeristy. Available at http://www.cad.iastate.edu/corn/inbreds
Collection date
2011
Collected by
Dow AgroSciences
Location
Ithaca, NY 14850
Plant structure
Leaf
Developmental stage
seedling
Sequencing and Assembly Information
Assembly name
Zm-B104-DRAFT-ISU_USDA-0.1
Assembly date
2012-05-01
WGS accession
Sequencing description
Sequence service provider: Dow AgroSciences Sequencing technologies: Illumina paired end sequencing Sequencing method: Illumina pair-end sequencing (50x) technology was used to sequence the B104 maize line followed by its genome assembly using a reference-guided approach with B73 as the reference genome. De novo assembly was used for assembling the unmapped Illumina reads. Draft beta pseudomolecule assembly was done using reference-guided assembly via ALLMAPS with B73 and W22 synteny markers generated with SynMap using the Ensembl B73 version 4.32 genome or the W22 genome vs the unassembled B104 scaffolds. Many scaffolds with annotations are still unplaced. Additionally, in the upcoming full-release, 20x PacBio reads are being generated to create pseudomolecules. Sequencing hardware: HiSeq2000 Genome coverage: 50X
Assembly description
Assembly methods: Reference based assembly plus de novo assembly for unmapped reads Construction of pseudomolecules: Yes
Reference Based scaffold assembly based on B73 genome v2 version. Pseudomolecule assembly using B73 v4 and W22.
Seq service provider
Dow AgroSciences
Assembly statistics
Scaff num
407,410
Perc seq scaffold
84.80
Perc seq unscaffold
15.20
Total scaff length
2,270,000,000 bp
Longest scaff
2,021,246 bp
Shortest scaff
201 bp
N50 scaff length
6,422 bp
N50 scaff count
21,663
N90 scaff length
5,567 bp
N90 scaff count
359
Total contig length
2,256,653,983 bp
Longest contig
469,437 bp
N50 contig length
32,474 bp
N50 contig count
18,287
N90 contig length
2,363 bp
N90 contig count
105,178
Total number of scaffolds in assembly.
% assembly in scaffolded contigs.
% assembly in UNscaffolded contigs.
Total sequence length represented by scaffolds.
Longest scaffold in assembly.
Shortest scaffold in assembly.
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 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.
