GC-Scaf-stats

Defined in file genome_collection.asn
C++ class: CGC_Scaf_stats


GC-Scaf-stats ::= SEQUENCE {
    --NOTE: These values equal to the stats_cd values in CodeStatistics table in GenomeColl
    stats-category  INTEGER {
        replicon-count (70),
        scaffold-count (22),
        component-count (23),-- How many components
        component-span-count (24),-- How many placements of components
        total-length (1),
        ungapped-length (2),
        min-gapped-scaf-length (25),
        max-gapped-scaf-length (26),
        min-ungapped-scaf-length (27),
        max-ungapped-scaf-length (28),
        active-finishing-bases (3),
        draft-bases (5),
        finished-bases (7),
        whole-genome-finishing-bases (9),
        other-sequences (11),
        pre-draft (13),
        wgs-bases (15),
        bases-in-spanned-gaps (17),
        n50 (19),
        spanned-gaps (20),
        unspanned-gaps (21),
        bases-in-unspanned-gaps (29),
        count-contig (30),  -- contig count
        contig-n50 (31),  -- contig N50
        contig-L50 (32),  -- contig L50
        contig-n75 (33),  -- contig N75
        contig-n90 (34),  -- contig N90
        scaf-L50 (35),  -- scaffold L50
        scaf-n75 (36),  -- scaffold N75
        scaf-n90 (37),  -- scaffold N90
        gc-count (38),  -- base counts for G,C
        atgc-count (39),  -- base count for A,T,G,C
        gc-perc (40),   -- gc-count / atgc-count as percentage.
        is-there-unplaced-scaf (72), -- 1 means there is unplaced scaffold. 0 means none
        count-singleton-unordered-scaffold (73),
        count-chr-made-of-singleton-ordered-scaffold (74),
    -- GCOL-675 - assembly release review stats. Meaningful only at assembly
    -- level.
        -- Do any of the chromosomes have a single component each?
        --   if yes, do all chromosomes have single component each?
        count-chr-with-single-component (75), -- INTEGER OPTIONAL,
        -- number of unplaced/unlocalized singleton scaffolds in minus orientation
        count-singleton-in-minus-orientation (76),-- INTEGER OPTIONAL,
        --chr-terminal-gap-types SET OF GC-ChrGapTypes OPTIONAL,
        -- are any gaps flagged as 'unknown' and how many? 0 means none.
        count-unknown-gaps (80), --  INTEGER OPTIONAL,
        -- 1.2c Scaffold source names: count implicit/explicit
        count-implicit-scaf-src-name (82), -- INTEGER OPTIONAL,
        count-explicit-scaf-src-name (83), -- INTEGER OPTIONAL
        all-chr-has-single-component (84), -- if 1 yes, 0 no. BOOLEAN OPTIONAL,
        -- Do any scaffolds have terminal gaps? How many?
        count-scaf-with-terminal-gaps (85), -- INTEGER OPTIONAL,
        -- Do any chromosome have terminal gaps? what is the gap type for each?
        count-chr-with-terminal-gaps  (86), -- INTEGER OPTIONAL,
        -- Number of component GIs (uniq components). Is the count different from the count in the
        -- latest GenBank/Refseq release for the same assembly, by how many?
        count-uniq-components (87), --INTEGER OPTIONAL ,
        count-uniq-component-diff-from-last-release (88), --INTEGER OPTIONAL,
        count-chromosome-types (89), --INTEGER OPTIONAL,
        count-chromosome-terminal-gap-types (90), -- # of chromosome terminal gap types
        count-dropped-components (91), -- dropped component due to foreign screen
        count-non-chromosome-replicon (92), -- number of non-Chromosome replicons
        count-assembly-units (93), -- # of assembly-units
        count-alt-loci-units (94), -- # of alt-loci units
        count-fixed-patches (95),  -- # of fixed patches
        count-novel-patches (96),  -- # of novel patches
        count-regions (97),        -- # of regions
        count-patches (98),        -- # of patches
        count-par-regions (99),    -- # of PAR regions
        count-genomic-regions (100), -- # of genomic regions
        count-chromosome-replicons (101), -- # of chromosomal replicons
        assembly-status (102), -- Assembly status 1 - Contig only;2 - Unplaced scaffolds only; 3 - Some chromosomes assembled;
                    -- 4 - all chromosomes assembled; 5 - complete sequence genome; 6-unlocalized and unplaced scaffolds.
        net-count-scaffold (103),  -- number of scaffolds that are not also chromosomes (22 - 75)
        net-count-component (104), -- number of components that are not also chromosomes or scaffolds (30 - 75 -73)
        count-regions-contain-alt-loci (105), -- number of regions containing alt-loci
        count-regions-contain-fix-patch (106), -- number of regions containing fix patch
        count-regions-contain-novel-patch (107), -- number of regions containing novel patch
        count-fix-patch-with-alignment (108), -- number of fix patch with alignment to primary assembly
        count-novel-patch-with-alignment (109), -- number of novel patch with alignment to primary assembly
        count-alt-scaf-with-alignment (110), -- number of alt scaffolds with alignment to primary assembly
        count-alt-loci-scaf (111), -- number of alt-loci scaffolds.
        count-real-scaffolds (112), -- number of scaffolds with gb_is_skipped = 0.
        top-level-count (113), -- Number of chromosomes or plasmids, unplaced/unlocalized scaffolds, alt-loci scaffolds, and patch scaffolds
        total-gap-length (114), -- Total length of gaps
        count-replicons-without-ordered-scaf (115), -- count of replicons without ordered scaffold

        other (255) -- catch all
    },
    value INTEGER
}