tbl_value_classes

Analytical value class describing a data column or measurement family.

Specifies a value class describing e.g. a data column

Dendrochronology value classes

value_class_id	value_type_id	parent_id	name	description
1	8	NULL	Tree species	Species name of the tree the sample came from.
2	1	NULL	Tree rings	Number of measured tree rings inferred as years.
3	12	NULL	Earlywood/Latewood	A notation in case the outermost ring is not complete. +ew in case only earlywood is present, -lw in case some part of the latewood is missing
4	1	NULL	Number of analysed radii.	Number of analysed radii.
5	3	NULL	EW/LW measurements	Record of whether the earlywood and latewood of each ring has been measured separately.
6	1	NULL	Sapwood (Sp)	Number of sapwood rings, which is the outer layers of a tree, between the heartwood and cambium.
7	3	NULL	Bark (B)	Whether bark was present in the sample.
8	13	NULL	Waney edge (W)	The last formed tree ring before felling or sampling. Presence of this represents the last year of growth.
9	1	NULL	Pith (P)	Number of rings missing between the core of the tree and the first measured ring.
10	5	NULL	Tree age ≥	The analysed age of the tree.
11	5	NULL	Tree age ≤	The analysed age of the tree.
12	6	NULL	Inferred growth year ≥	The growth year inferred from the analysed tree rings.
13	6	NULL	Inferred growth year ≤	The growth year inferred from the analysed tree rings.
14	10	NULL	Estimated felling year	The felling year as inferred from the analysed outermost tree-ring date
15	10	NULL	Possible estimated felling year	Used for samples where dating has not been succesful but a non-statistically satisfactory dating suggestion is given.
16	7	NULL	Provenance	The provenance of the sampled tree, inferred by comparing the sample with others.
17	10	NULL	Outermost tree-ring date	The date of the outermost tree-ring
18	3	NULL	Not dated	Used to mark samples as not having been succesfully dated, i. e. analysed but not dated
19	7	NULL	Date note	Notes on  a sample.
20	7	NULL	Provenance comment	Comments on the provenance of a sample
21	1	NULL	Non-measured tree rings	Estimated number of non-measured tree rings outside the outermost measured tree ring.
22	1	NULL	Non-measured sapwood rings	Estimated number of non-measured sapwood rings outside the outermost measured tree ring1
24	10	NULL	Innermost tree-ring date	The date of the innermost tree-ring
23	1	6	Sapwood indicator	Indicates if sample has sapwood, which is the outer layers of a tree, between the heartwood and cambium.

Ancient DNA analysis value classes

value_class_id	value_type_id	parent_id	name	description
43	17	NULL	Molecular sex - Rx	Prediction of molecular sex of individual. Rx is based on the ratio of reads aligning to the X chromosome and autosomes.
42	9	NULL	mtDNA haplogroup	Prediction of mitochondrial DNA haplogroup.
41	9	NULL	Y haplogroup	Prediction of Y chromosome haplogroup.
40	9	NULL	1st deg. relatives	List of sample IDs that are 1st degree relatives to the analysed individual.
39	9	NULL	2nd deg. relatives	List of sample IDs that are 2nd degree relatives to the analysed individual.
38	9	NULL	>2nd deg. relatives	List of sample IDs that are further than 2nd degree relatives to the analysed individual.
37	14	NULL	Library preparation(s)	Type of sequence library preparation (e.g. blunt-end, single-stranded, etc.).
36	16	NULL	Damage treatment(s)	Type of damage treatment if applicable (e.g. UDG).
35	15	NULL	SNP capture	Type of SNP capture if applicable (e.g. 1240k).
34	7	NULL	Metagenomics analysis	Record of whether the library been subjected to a metagenomic analysis.
54	9	NULL	Organism genome mapped to	Organism whose reference sequence / genome assembly was used for sequence alignment.
53	9	NULL	Reference genome assembly	reference sequence / genome assembly name or accession code.
52	1	NULL	Endogenous reads (filtered)	The number of sequence reads which have successfully mapped to the organism reference sequence after filtering.
51	11	NULL	Average read length	The average length of mapped sequence reads, excluding reads shorter than 35 bases and reads with less than 90% consensus to the species reference.
50	11	NULL	Average depth of coverage - genome (x)	The number of times on average that a given nucleotide in the genome has been sequenced.
49	4	NULL	Breadth of coverage - genome (%)	The percentage of the reference sequence / genome assembly covered after alignment.
48	11	NULL	Average depth of coverage - mtDNA (x)	The number of times on average that a given nucleotide in the mitochondrial genome has been sequenced.
47	2	NULL	mtDNA reads	The number of sequence reads which have successfully mapped to the mitochondrial DNA in the reference sequence.
46	2	NULL	X chromosome reads	The number of sequence reads which have successfully mapped to the X chromosome in the reference sequence.
45	1	NULL	Y chromosome reads	The number of sequence reads which have successfully mapped to the Y chromosome in reference sequence.
44	17	NULL	Molecular sex - Ry	Prediction of molecular sex of individual. Ry is based on the ratio of reads aligning to the X and Y chromosomes.
33	9	NULL	General library file name	General file name suffix for library DNA sequence fastq files, BAM files, etc.
32	1	NULL	Merged reads	The total number of merged sequence reads retained following adapter removal and merging of read pairs.
31	2	NULL	Endogenous reads (raw)	The number of sequence reads which have successfully mapped to the organism reference sequence before filtering.
30	4	NULL	Raw endogenous content (%)	The number of sequence reads which have successfully mapped to the organism reference sequence after filtering.
29	4	NULL	Duplicate reads (%)	The percentage of mapped sequence reads that are PCR duplicates i.e. they have identical start and end positions.
28	4	NULL	Short reads (%)	The percentage of mapped sequence reads that are shorter than 35 bases.
27	11	NULL	5’ damage	Proportion of T nucleotides (given C nucleotide in reference) at the 5’ end of sequence reads. Representative of damage to DNA due to deamination of cytosines.
26	11	NULL	3’ damage	Proportion of A nucleotides (given G nucleotide in reference) at the 3’ end of sequence reads. Representative of damage to DNA due to deamination of cytosines on complementary strand.
25	7	NULL	Methods metadata download link	Link to methods metadata worksheet (with lab and bioinformatics methods, tools, parameters, etc.).