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-LH244-REFERENCE-BAYER-1.0
Assembly identifier: Zm00052a
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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.
Sequence, assembly and annotation of Bayer Crop Science’s maize inbred line LH244.
Tom Slewinski, Ruth Wagner, Phil Taylor, Graziana Taramino, Charles Armstrong, Shubha Subbarao, John LeDeaux, Zane Goodwin, Keith Decker, Matthew Dimmic, Crystal Ruth, Ericka Havecker, Mitch Sudkamp, Paul Chomet, Guy Kol, Omer Barad, Kobi Baruch, Shawn Kaeppler, Mike Peterson
Assembly methods: NRGene Construction of pseudomolecules: NRGene
Finishing strategy
NRGene
Assembly statistics
Scaff num
40,302
Perc seq scaffold
100.00
Total scaff length
2,250,279,090 bp
Longest scaff
36,803,518 bp
Shortest scaff
257 bp
N50 scaff length
6,890,988 bp
N50 scaff count
93
N90 scaff length
1,245,217 bp
N90 scaff count
368
Total contig length
2,203,812,633 bp
Longest contig
616,394 bp
Shortest contig
128 bp
N50 contig length
80,917 bp
N50 contig count
8,063
N90 contig length
17,754 bp
N90 contig count
29,291
Total number of scaffolds in assembly.
% assembly in scaffolded 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 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
Zm00052a.1
Annotation Provider
Bayer Crop Science
Annotation Date
9/12/2019
Is current
yes
Annotation Software
MAKER-P, MIKADO, Augustus, SNAP
Annotation Description
MAKER-P gene prediction with Augustus and SNAP was based on transcript evidence from Genbank cDNA, Illumina transcript assemblies and Pacbio Isoseq and protein evidence from Arabidopsis, rice, sorghum, Setaria, and Brachypodium. Additional gene models created by high quality IsoSeq transcript alignments and Transdecoder gene predictions were combined with the MAKER-P gene set using MIKADO.
Metadata
Browser
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