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Information about assembly Zm-CML247-DRAFT-PANZEA-1.0    (also known as CML247)
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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   2017
   Browse Genome   Genome browser at MaizeGDB
   Data download   http://ftp.maizegdb.org/MaizeGDB/FTP/CML247/
   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
   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
   Sequencing description   Sequencing technologies: Illumina HiSeq2500, Illumina MiSeq
Sequencing method: Illumina HiSeq2500, Illumina MiSeq
   Assembly description   Assembly methods: DenovoMAGIC
   Browse Genome   Genome browser at MaizeGDB
   Data download   http://ftp.maizegdb.org/MaizeGDB/FTP/CML247/
   Release date   2017
   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.

Annotation

   Annotation Identifier   Zm00006a.1
   Annotation Provider   Yingping Jiao, Ware lab at CSHL
   Annotation Date   October, 2016
   Annotation Download   http://ftp.maizegdb.org/MaizeGDB/FTP/CML247/