Data Template
Template TypeMARKER
Templatemarker
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Headers
ColumnDescription
* marker_nameName of the marker.
* marker_typeMarker type such as SSR, RFLP, RAPD, STS, SCAR, overgo probe and Isozyme. Refer to the available marker_type page for each database.
* genusThe genus name of the organism from which the marker was developed.
* speciesThe species name of the organism from which the marker was developed. Enter 'sp.' to represent one unknown species, 'spp.' to represent multiple unknown species.
infraspecific_typeInfraspecific type of the stock as defined in the taxonomic_rank CV
infraspecific_nameInfraspecific name of the stock
aliasOther names used for the marker. Multiple aliases, separated by a semicolon (;), can be added.
marker_locusName of the marker locus. Multiple loci, separated by a semicolon (;), can be added..
marker_sequenceSequence of the marker when available. For SNP, it should be in the format of 5'flanking sequence[A/T] 3'flanking sequence.
GB_IDAssociated GenBank ID of the marker or the source of the marker (eg. EST).
dbSNP_IDAssociated dbSNP_ID. The submitted SNPs (SS) number should be used.
RS_IDThe refSNP (RS) number.
geneAssociated genes.
mRNAAssociated mRNAs.
five_prime_flanking_seq5' flanking sequence of SNP or Indel.
three_prime_flanking_seq3' flanking sequence of SNP or Indel.
shared_speciesSpecies names of organisms that have been found to have the same SNP. If there are more than one other species, using ';' to separate.
repeat_motifRepeat motif for SSR markers.
snp_chip_nameSNP chip name when SNPs belong to a chip (the name should match 'name' in Library sheet.
snp_chip_idSNP chip ID if there is a specific ID for the specific SNP chip entered in 'SNP_chip_ID'.
restriction_enzymeRestriction Enzyme used for CAPS marker or other markers that use restriction enzymes.
product_lengthThe PCR product length from the source species of the marker.
max_lengthThe maximum product size that have been observed.
min_lengthThe minimum product size that have been observed.
is_codominantYes if the marker is codominant, No otherwise.
PCR_conditionPCR condition for PCR-based markers.
screening_methodGel type, % etc (eg. 2% agarose) for PCR product visualization and any other screening methods for other types of markers.
monomorphic_populationThe name of the mapping population of which the marker was monomorphic.
source_marker_nameThe name of the marker from which the marker is generated (STS, SSR or SCAR markers are often generated from other markers). The detail of the source marker should be given in a separate row.
source_descriptionWhether the marker was developed from the sequence of EST, BAC, cDNA, genomic clone, or WGS.
indel_seqsequences of indel (eg. ATT).
allelesAlleles for the SNP marker (eg. A/T).
gel_picture_file_nameFile name of the gel picture if available.
gel_picture_legendLegend of the gel picture if available.
commentsAny comments about the marker.
varietyThe variety from which the marker was developed. It should match a 'stock_name' in the Stock sheet.
imageImage_ID of any associated image (Detailed info in 'Image' sheet.) Multiple images, separated by comma, can be added.
contactContact person for the marker (Please provide the contact info of these researchers in 'Contact' sheet).
referenceReference where the marker is originally described (pub_id), Multiple references, separated by comma, can be added.
~identifierSpecial columns to store names and sequences of primers and probes. The column name should start with ~. An identifier must be either 'primer' or 'probe' , followed by a numerical number and 'name' or 'seq'. (e.g.) primer1_name, primer1_seq, primer2_name, primner2_seq ; probe1_name, probe1_seq, probe2_name, probe2_seq (More columns can be created when there are more than two primers and probes).
##property_nameSpecial columns (##) : followed by name (cvterm name) of the property.
* Required field