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     Quick Answer


    N50 value (genome assembly contiguity metric)
    N50 is the contig/scaffold length such that 50% (by total assembled length) of the genome assembly is contained in contigs/scaffolds of that length or longer—i.e., a higher N50 generally indicates more contiguous assemblies.
    Example reported values in recent assemblies: sugar beet RefBeet-3.0 contig/scaffold N50 = 61.5 Mb and Magnolia zenii contig N50 ≈ 85.1 Mb.
    See cited sources for exact reported N50s.



     Long Answer


    N50 value — what it is (and why people report it)
    N50 is a genome assembly contiguity metric: the length L such that 50% of the assembly’s total length is contained in contigs/scaffolds of length ≥ L (with lengths sorted from longest to shortest).
    How to read N50 (important caveats)
    • N50 is unit- and context-dependent: you may see contig N50 (pre-Hi-C) and scaffold N50 (post-Hi-C / chromosome scaffolding). A scaffold N50 is not automatically “more accurate” than contig N50—only more length-compact under the chosen scaffolding scheme.
    • Higher N50 usually means fewer/longer fragments, but it can also reflect choices in scaffolding, gap handling, or repeat resolution—so N50 should be interpreted alongside completeness/accuracy metrics (e.g., BUSCO, read mapping).
    • Single-number bias: N50 is not a complete quality guarantee—an assembly can have high N50 but still contain misassemblies or missing regions.
    N50 values reported in the provided assemblies (from raw paper-reported metrics)
    The bars below show reported N50 values (in Mb) from the included full-text research records. Where a paper reports both contig N50 and scaffold N50, both are included.
    Direct mapping: which paper reports which N50?
    Below is a compact table of the N50 values used in the plot.
    Paper record Contig N50 Scaffold N50 Genome/assembly type context (as reported) Evidence
    RefBeet-3.0 (sugar beet genotype KWS2320) 61.5 Mb 61.5 Mb Long-read reference assembly (PacBio + optical mapping + polishing)
    Magnolia zenii (near telomere-to-telomere assembly) ~85.1 Mb ~86.6 Mb HiFi + ONT + Hi-C; chromosome-scale assembly
    Istocheta aldrichi (tachinid parasitoid fly) 4.77 Mb — ONT/PacBio-based assembly; scaffolds reported without scaffold N50 in record excerpt
    Myrmica angulata (ant) 1.752 Mb 18.23 Mb PacBio + Illumina + Hi-C; chromosome-level scaffolding
    Eocanthecona furcellata (predatory stink bug) 2.35 Mb 135.69 Mb HiFi + Hi-C; organized into pseudochromosomes
    Acropora intermedia (reef coral) 2.9 Mb — PacBio HiFi-based re-annotation; contig contiguity emphasized in record
    Fraxinus mandshurica (telomere-to-telomere) 34.29087 Mb 34.29087 Mb HiFi + Hi-C telomere-to-telomere assembly; chromosome-level (23 chromosomes)
    Inline evidence for each N50 figure used in the plot:
    • RefBeet-3.0 reports N50 = 61.5 Mb.
    • Magnolia zenii reports contig N50 ≈ 85.1 Mb and scaffold N50 ≈ 86.6 Mb in the provided record.
    • Istocheta aldrichi reports assembly N50 = 4.77 Mbp.
    • Myrmica angulata reports contig N50 = 1.752 Mb and scaffold N50 = 18.23 Mb.
    • Eocanthecona furcellata reports contig N50 = 2.35 Mb and scaffold N50 = 135.69 Mb.
    • Acropora intermedia reports contig N50 = 2.9 Mb.
    • Fraxinus mandshurica reports contig N50 = 34.29 Mb (and scaffold N50 reported equal in the provided record).
    If you need to compare N50 across papers
    • Compare contig N50 vs scaffold N50 only within the same assembly strategy (e.g., both with Hi-C scaffolding).
    • Check whether N50 is influenced by gap filling, telomere extension, or scaffold curation (these change the set of lengths contributing to the cumulative 50% threshold). (This point follows from the definition and the fact that assembly processing changes contig/scaffold length distributions; QUAST’s framework positions N50 among other QC metrics rather than as a standalone truth.)


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    Updated: March 25, 2026

     Top Data Sources ExportMCP


     Analysis Wizard



    It would compute N50 from a list of contig/scaffold lengths (sorted descending, cumulative sum until 50% of total length), then generate contig-vs-scaffold plots from the paper-reported values.



     Hypothesis Graveyard


    “Higher N50 always means higher biological accuracy.” This fails because N50 is contiguity-only; pipeline choices can inflate N50 without improving correctness, so accuracy must be triangulated with other QC metrics.


    “N50 is comparable across all assembly tools and genomes.” This is unlikely: N50 depends on assembly level (contig vs scaffold) and preprocessing/curation choices, making apples-to-apples comparisons nontrivial.

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