Genotype API Documentation - v0.1.0
    Preparing search index...

    Interface SequenceStats

    Comprehensive sequence statistics result

    Contains all statistical metrics calculated from a set of sequences, including length distributions, composition analysis, and quality metrics.

    interface SequenceStats {
        file?: string;
        format: "FASTA" | "FASTQ" | "Mixed" | "Unknown";
        type: "DNA" | "RNA" | "Unknown" | "Protein";
        numSequences: number;
        totalLength: number;
        minLength: number;
        maxLength: number;
        avgLength: number;
        n50?: number;
        n90?: number;
        q1Length?: number;
        q2Length?: number;
        q3Length?: number;
        gcContent?: number;
        gapCount?: number;
        ambiguousCount?: number;
        baseComposition?: {
            A: number;
            T: number;
            G: number;
            C: number;
            U: number;
            N: number;
            other: number;
        };
        avgQuality?: number;
        minQuality?: number;
        maxQuality?: number;
        q20Percentage?: number;
        q30Percentage?: number;
        qualityEncoding?: QualityEncoding;
    }
    Index

    Properties

    file? format type numSequences totalLength minLength maxLength avgLength n50? n90? q1Length? q2Length? q3Length? gcContent? gapCount? ambiguousCount? baseComposition? avgQuality? minQuality? maxQuality? q20Percentage? q30Percentage? qualityEncoding?

    Properties

    file?: string

    File or data source identifier

    format: "FASTA" | "FASTQ" | "Mixed" | "Unknown"

    Detected format of sequences

    type: "DNA" | "RNA" | "Unknown" | "Protein"

    Inferred sequence type based on content

    numSequences: number

    Total number of sequences processed

    totalLength: number

    Sum of all sequence lengths

    minLength: number

    Shortest sequence length

    maxLength: number

    Longest sequence length

    avgLength: number

    Average sequence length

    n50?: number

    N50 - length where 50% of bases are in sequences >= this length

    n90?: number

    N90 - length where 90% of bases are in sequences >= this length

    q1Length?: number

    First quartile length

    q2Length?: number

    Median length (second quartile)

    q3Length?: number

    Third quartile length

    gcContent?: number

    Overall GC content (0.0 to 1.0)

    gapCount?: number

    Number of gap characters (-, ., *)

    ambiguousCount?: number

    Number of ambiguous bases (N, R, Y, etc.)

    baseComposition?: {
        A: number;
        T: number;
        G: number;
        C: number;
        U: number;
        N: number;
        other: number;
    }

    Base composition counts

    avgQuality?: number

    Average quality score across all bases

    minQuality?: number

    Minimum quality score found

    maxQuality?: number

    Maximum quality score found

    q20Percentage?: number

    Percentage of bases with quality >= 20

    q30Percentage?: number

    Percentage of bases with quality >= 30

    qualityEncoding?: QualityEncoding

    Quality encoding detected or specified

    Settings

    Member Visibility

    On This Page

    Properties