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<h3>GC-Scaf-stats</h3><pre>Defined in file <a href="genome_collection.asn.html">genome_collection.asn</a>
C++ class: <a href="../doxyhtml/classCGC__Scaf__stats.html">CGC_Scaf_stats</a>
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), -- <a href="Assembly.html">Assembly</a> 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
}</pre>
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