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Information about assembly Zm-B104-DRAFT-ISU_USDA-0.1    (also known as B104)
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Genome Sequencing Project Information
   The B73 inbred line is the source of our community reference genome. However, B73 cannot be transformed, making it difficult to make use genomic data for genetics studies that involve transformation. Our motivation was to identify an inbred line similar to B73 for plant transformation. Both B73 and B104 are derived from the Iowa Stiff Stalk Synthetic lines. Unlike B73, B104 is readily transformed. The ISU Plant Transformation Facility now offers transformation services for the B104 inbred line. They share about 93% similarity as calculated using TIPSimSelector at MaizeGDB, a tool that assess genetics similarity based on methods described in Romay et al., 2013
   This sequence has been released under the Toronto Agreement. No whole-genome research may be submitted for publication until the official publication for this genome assembly has been published.
   Project PI   Carolyn Lawrence-Dill
   Project start date   2012
   Release date   fall 2017
   Browse Genome   Genome browser at MaizeGDB
   Data download   https://ftp.maizegdb.org/MaizeGDB/FTP/Zm-B104-DRAFT-ISU_USDA-0.1/
   Publication status   Pending

Stock and Biosample Information
Stock information
   Stock name   cultivar:B104
   Stock record   113829
   Stock details   cultivar:B104
   Stock provided by   Iowa State University
Biosample information
   Sample description   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
   Plant structure   Leaf
   Developmental stage   seedling

Sequencing and Assembly Information
   Assembly name   Zm-B104-DRAFT-ISU_USDA-0.1
   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
   Assembly description   Assembly methods: Reference based assembly plus de novo assembly for unmapped reads
Construction of pseudomolecules: Yes
   Browse Genome   Genome browser at MaizeGDB
   Data download   https://ftp.maizegdb.org/MaizeGDB/FTP/Zm-B104-DRAFT-ISU_USDA-0.1/
   Release date   fall 2017
   Sequencing method   Illumina paired end sequencing
   Finishing strategy   Draft
   Seq hardware   HiSeq2000
   Genome used for alignment   Reference Based scaffold assembly based on B73 genome v2 version. Pseudomolecule assembly using B73 v4 and W22.
   Genome coverage   50X
   Seq service provider   Dow AgroSciences
Assembly statistics
   Scaff num   407,410
   Perc seq scaffold   85
   Perc seq unscaffold   15
   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.

Annotation
   Annotation Identifier   Zm00007a.1
   Annotation Provider   Buckler lab
   Annotation Software   MAKER-P 2.31.8
   Annotation Download   http://ftp.maizegdb.org/MaizeGDB/FTP/B104/Pseudomolecule_Assembly/