Container element of a DNA sample containig information about DNA extraction, PCR amplifications, cloning and sequencing
Method or protocol used for secundary purification of already extracted genomic DNA
Ratio of absorbance at 260 nm and 280 nm used to assess the purity of DNA (mainly proteins, phenol and others)
Ratio of absorbance at 260 nm and 230 nm assessing DNA purity (mostly secundary measure, indicates maily EDTA, carbohydrates, phenol)
DNA concentration value
Method used for determination of concentration and ratio of absorbance parameters
DNA volume value
DNA weight value
Method used for determination of DNA weight
Date when DNA or tissue quality parameters were determined
Sample quality estimation based on parameters described at QualityRemarks
Description of methods and parameters defining low, medium or high quality of a sample
Result of DNA-DNA hybridization, e.g. strain: measurement value percentage
result of melting temperature (Tm) analysis, e.g. measurement value unit
MIxS element. The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. e.g. 300000 bp; Already in MIGS/MIMS 7-12-10 but not in MIMARKS 26-1-11.
MIxS element. Pooling of DNA extracts (if done). were multiple DNA extractions mixed? how many?
Container element for information on images of the DNA sample (e.g. agarose gel images)
Link to an DNA sample image (e.g. agarose gel image)
Container element for infomation of all amplifications
Container element for information related to an individual amplification
Container element for individual amplifications
Date when the amplification was carried out
Person or Institution who performed the amplification
Marker, genetic locus or DNA fragment amplified by PCR (e.g. "CO1", "ITS").
Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA e.g. V6, V9, ITS
true/false or yes/no whether the ampliciation was sucessful in general
details about the amplification, e.g. including why it has failed
Method used for amplification. Similar to MIxS term: pcr_conditions.
Method or protocol used to purify the PCR product
MIxS element "library reads sequenced". Total number of clones sequenced from the library
MIxS element "library screen". Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences e.g. enriched, screened, normalized
MIxS element "library size". Total number of clones in the library prepared for the project
MIxS element "library vector". Cloning vector type(s) used in construction of libraries
MIxS element "library construction method". Library construction method used for clone libraries e.g. paired-end,single,vector
Name of Plasmid used for sequencing.
Container element for all DNA sequencings (related to all sequences and sequencing runs of one fragment or locus)
Container element for all sequencing information related to a defined clone of a cloned fragment (contains only one element if the fragment was not cloned)
Container element for amplification primers
Container element for an individual amplification primer
Container element for DNA sequencings
Date when the DNA cloning was carried out
Person or institution which performed DNA cloning
Method or protocol used for DNA cloning
Name of the individual DNA clone
Container element for amplification primers
Container element for an individual cloning primer
guanine-cytosine content in mol %
Container element for all individual DNA sequencings (related to all sequnecing runs of a defined clone of a cloned fragment)
Container element for information related to an individual sequencing (related to a unique sequencing run)
Consensus sequence derived from all individual sequences
Length of the consensus sequence (number of base pairs)
Link to the chromatogram of the consensus sequence
DNA Barcode sequence (part or 100% of the consensus sequence)
MIxS element. A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point
MIxS element How was the assembly done (e.g. with a text based assembler like phrap or a flowgram assembler etc). Input: CV
MIxS element Relevant standard operating procedures.
MIxS element Was the genome project intended to produce a complete or draft genome, Coverage, the fold coverage of the sequencing expressed as 2x, 3x, 18x etc, and how many contigs were produced for the genome
MIxS element. For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
Result of comparison of two markers of two specimens or strains. Name or TAX-ID (NCBI) of compared specimens/strain and the relative identity percentage must be given.
MIxS element "sequence quality check". Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA e.g. none or manually edited
Name of the haplotype, if applicable
Container element for the genetic accession number
Definite number or ID under which the DNA sequence is deposited in a public database (e.g. GenBank accession number)
Link to the related record in a public database (e.g. link to a GenBank or EMBL record)
Definite number or ID under which the DNA sequence is deposited in the BOLD database
Container element for references to DNA sequences or the consensus sequence
Container element for references to individual DNA sequences or the consensus sequence
Container element for information on individual sequences/reads
Direction of sequencing/read (e.g. forward, reverse)
Date when the DNA sequence/read was produced
Person or institution which performed the sequencing/read
Method or protocol used to generate the DNA sequences/reads
Sequence of the individual DNA sequence/read (A,T,G,C; 5' to 3')
Length of the single sequence/read (Number of base pairs)
Length of fragments (on average or precise)
Link to the chromatogram of an individual DNA sequence (single read)
Container element for all sequencing primers
Container element for an individual sequencing primer
Container element for an reference to DNA sequences or the consensus sequence
Reference to DNA sequences or the consensus sequence
Link to the reference for DNA sequences or the consensus sequence
Container element for information of a sequencing or amplification primer
DNA sequence of the primer (A,T,G,C; 5' to 3')
Name of the primer
First reference of the primer
Link to the first reference of the primer
MIxS element. Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters e.g.adapter A and B sequence
MIxS element. Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters.
String, extended with Type attribute
String, extended with direction attribute (e.g. 'forward' or 'reverse')
String, extended with Unit attribute (e.g. ng/µl, µl, ng)