Sequencing and Assembly Information |
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Assembly name |
Zm-B104-DRAFT-ISU_USDA-0.1 |
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WGS accession |
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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 |
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Assembly description |
Assembly methods: Reference based assembly plus de novo assembly for unmapped reads
Construction of pseudomolecules: Yes |
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Browse Genome |
Genome browser at MaizeGDB |
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Data download |
https://download.maizegdb.org/Zm-B104-DRAFT-ISU_USDA-0.1
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Release date |
fall 2017 |
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Sequencing method |
Illumina paired end sequencing |
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Finishing strategy |
Draft |
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Seq hardware |
HiSeq2000 |
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Genome used for alignment |
Reference Based scaffold assembly based on B73 genome v2 version. Pseudomolecule assembly using B73 v4 and W22. |
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Genome coverage |
50X |
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Seq service provider |
Dow AgroSciences |
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| Assembly statistics |
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Scaff num |
407,410 |
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Perc seq scaffold |
85 |
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Perc seq unscaffold |
15 |
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Total scaff length |
2,270,000,000 bp |
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Longest scaff |
2,021,246 bp |
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Shortest scaff |
201 bp |
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N50 scaff length |
6,422 bp |
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N50 scaff count |
21,663 |
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N90 scaff length |
5,567 bp |
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N90 scaff count |
359 |
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Total contig length |
2,256,653,983 bp |
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Longest contig |
469,437 bp |
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N50 contig length |
32,474 bp |
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N50 contig count |
18,287 |
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N90 contig length |
2,363 bp |
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N90 contig count |
105,178 |
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Total number of scaffolds in assembly.
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% assembly in scaffolded contigs.
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% assembly in UNscaffolded contigs.
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Total sequence length represented by scaffolds.
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Longest scaffold in assembly.
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Shortest scaffold in assembly.
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The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 50% of the total assembly size.
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How many scaffolds are counted in reaching the N50 threshold.
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The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 90% of the total assembly size.
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How many scaffolds are counted in reaching the N90 threshold.
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Total sequence length represented by contigs.
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The longest contig.
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The length of contig which takes the sum length (summing from longest to shortest contig) past 50% of the total assembly size.
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How many contig are counted in reaching the N50 threshold.
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The length of contig which takes the sum length (summing from longest to shortest contig) past 90% of the total assembly size.
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How many contig are counted in reaching the N90 threshold.
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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.
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