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.
TYPSimSelector: A tool that sorts identity-by-state values derived from SNP datasets for accessions in the Ames Diversity Panel (a USDA-maintained set of maize lines representing wide genetic variation in Ames, Iowa).
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.
Exceptional intra-specific gene order and gene structural variations between maize B73 and Mo17 genome.
Silong Sun, Yingsi Zhou, Jian Chen, Junpeng Shi, Haiming Zhao, Hainan Zhao, Weibin Song, Mei Zhang, Yang Cui, Xiaomei Dong, Han Liu, Xuxu Ma, Yinping Jiao, Xuehong Wei, Joshua C. Stein, Jeff C. Glaubitz, Fei Lu, Guoliang Yu, Chengzhi Liang, Kevin Fengler, Bailin Li, Antoni Rafalski, Patrick S. Schnable, Doreen H. Ware, Edward S. Buckler, Jinsheng Lai
DOI
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 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.
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
Zm00014ba.1
Annotation Provider
Jinsheng Lai, State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University
Annotation Date
2021-06-01
Is current
yes
Annotation Software
EVidenceModeler-1.1.1
Annotation Description
Gene annotation of the Mo17 genome was performed using GeMoMa, Mikado, PASA, and MAKER with evidence from protein homologies, RNA-seq, and/or ISO-seq, as well as using ab initio Fgenesh prediction. Gene models predicted by different approaches were combined by EvidenceModeler to obtain an optimal non-redundant set of gene annotation. After removing transposon genes, we obtained a total of 42,580 high-confidence protein-coding genes, of which 30,975 genes were supported by RNA-seq data with a threshold of at least 90% coverage for CDS.
