|
|
|
|
Information about assembly Zm-CML247-DRAFT-PANZEA-1.0
(also known as CML247)
|
|
|
Click
here
to learn about maize genome and gene model nomenclature rules.
|
|
|
|
|
|
Genome Sequencing Project Information |
|
| |
Genome assembly of tropical maize inbred line CML247. The genome is sequenced using Illumina HiSeq and MiSeq with depth of 130X. For CML247, also see http://www.maizegdb.org/data_center/stock?id=105100 |
|
| |
Project PI |
Fei Lu, Edward Buckler |
| |
Project start date |
2014 |
| |
Release date |
5/30/2016 |
| |
Browse Genome |
Genome browser at MaizeGDB |
| |
Data download |
https://ftp.maizegdb.org/MaizeGDB/FTP/Zm-CML247-DRAFT-PANZEA-1.0/
|
| |
Publication status |
published |
|
Project reference |
High-resolution genetic mapping of maize pan-genome sequence anchors.
Lu F, Romay MC, Glaubitz JC, Bradbury PJ, Elshire RJ, Wang T, Li Y, Li Y, Semagn K, Zhang X, Hernandez AG, Mikel MA, Soifer I, Barad O, Buckler ES
At MaizeGDB
DOI
|
|
|
|
|
|
|
|
|
|
|
Stock and Biosample Information |
|
| Stock information |
| |
Stock name |
PI 674445 |
| |
Stock record |
105100 |
| |
Stock details |
PI 674445 |
| |
Stock provided by |
Ithaca, NY 14850 |
|
|
| Biosample information |
| |
GenBank BioSample |
SAMN07427883 |
| |
Collection date |
2006 |
| |
Collected by |
Genomic Diversity, Institute of Biotechnology, Cornell University |
| |
Plant structure |
PO:0000003 |
| |
Developmental stage |
Seedling |
|
|
|
|
|
|
|
|
|
|
|
|
Sequencing and Assembly Information |
|
| |
Assembly name |
Zm-CML247-DRAFT-PANZEA-1.0 |
| |
WGS accession |
|
| |
Sequencing description |
Sequence service provider: Library Prep by University of Illinois / Sequenced by Cornell University
Sequencing technologies: Illumina HiSeq2500, Illumina MiSeq
Sequencing method: Illumina HiSeq2500, Illumina MiSeq |
| |
Assembly description |
Assembly methods: DenovoMAGIC
Construction of pseudomolecules: Scaffolds were ordered and oriented |
| |
Browse Genome |
Genome browser at MaizeGDB |
| |
Data download |
https://ftp.maizegdb.org/MaizeGDB/FTP/Zm-CML247-DRAFT-PANZEA-1.0/
|
| |
Release date |
5/30/2016 |
| |
Sequencing method |
Illumina HiSeq2500, Illumina MiSeq |
| |
Finishing strategy |
Complete genome |
| |
Genome coverage |
130x |
|
| Assembly statistics |
| |
Scaff num |
35,435 |
| |
Longest scaff |
16,681,975 bp |
| |
N50 scaff length |
2,592,978 bp |
| |
N50 scaff count |
253 |
| |
N90 scaff length |
523,911 bp |
| |
N90 scaff count |
947 |
|
|
Total number of scaffolds in assembly.
|
|
Longest 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.
|
|
|
|
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.
|
|
|
|
|
|
|
|
|
|
|
