Stock type being evaluated in this trial: accession Stock type being evaluated in this trial: accession

Stock type being evaluated in this trial: cross unique id Stock type being evaluated in this trial: cross unique id

Stock type being evaluated in this trial: family name Stock type being evaluated in this trial: family name

• plot_name (must be unique across entire database. This is often a concatenation of the trial name and the plot number.)
• accession_name or cross_unique_id or family_name (must exist in the database. This is the accession or cross unique id or family name being tested in the plot.)
• plot_number (a sequential number for the plot in the field (e.g. 1001, 1002, 2001, 2002). These numbers should be unique for the trial.)
• block_number (a design parameter indicating which block the plot is in)

• is_a_control (type 1 in this field if the plot is a control, otherwise leave blank. generally you will have accessions/cross unique ids/family names that are controls, so you should indicate the plots of those accessions/cross unique ids/family names as a control.)
• rep_number (replicate number, numeric)
• range_number (range number. often synonymous with col_number, numeric)
• row_number (row number. If the field is a grid, this represents the y coordinate, numeric, required for field map generation. the top left plot should be row 1, column 1)
• col_number (column number. If the field is a grid, this represents the x coordinate. Sometimes called range_number, numeric, required for field map generation. the top left plot should be row 1, column 1)
• seedlot_name (the seedlot from where the planted seed originated. Must exist in the database)
• num_seed_per_plot (number seeds per plot. Seed is transferred from seedlot mentioned in seedlot_name. Numeric)
• weight_gram_seed_per_plot (weight in gram of seeds in plot. seed is transferred from seedlot mentioned in seedlot name. Numeric)

• treatment columns (additional column(s) that specify the name of a treatment (e.g. inoculated, drought, etc). The value for each plot should be 1 if the treatment was applied or empty.)

trial_name,breeding_program,location,year,design_type,description,trial_type,plot_width,plot_length,field_size,planting_date,harvest_date,plot_name,accession_name,plot_number,block_number,is_a_control,rep_number,range_number,row_number,col_number,seedlot_name,num_seed_per_plot,weight_gram_seed_per_plot

• trial_name (Must be unique across entire database. It is often a concatenation of the year, purpose, unique number, and location.)
• breeding_program (The name of breeding program that managed the trial, must exist in the database.)
• location (The name or abbreviation of the location where the trial was held, must exist in the database.)
• year (The year the trial was held.)
• design_type (The shorthand for the design type, must exist in the database. Possible values include CRD (Completely Randomized Design), RCBD (Randomized Complete Block Design), RRC (Resolvable Row-Column), DRRC (Doubly-Resolvable Row-Column), ARC (Augmented Row-Column), Alpha (Alpha Lattice Design), Lattice (Lattice Design), Augmented (Augmented Design), MAD (Modified Augmented Design), greenhouse (undesigned Nursery/Greenhouse), splitplot (Split Plot), p-rep (Partially Replicated), Westcott (Westcott Design))
• description (Additional text with any other relevant information about the trial.)
• plot_name (Must be unique across entire database. It is often a concatenation of the trial name and the plot number.)
• accession_name (The accession being tested in the plot, must exist in the database.)
• plot_number (A sequential number for the plot in the field (e.g. 1001, 1002, 2001, 2002). These numbers should be unique for the trial.)
• block_number (A design parameter indicating which block the plot is in.)

• trial_type (The name of the trial type, must exist in the database. Possible values include Seedling Nursery, phenotyping_trial, Advanced Yield Trial, Preliminary Yield Trial, Uniform Yield Trial, Variety Release Trial, Clonal Evaluation, genetic_gain_trial, storage_trial, heterosis_trial, health_status_trial, grafting_trial, Screen House, Seed Multiplication, crossing_block_trial, Specialty Trial)
• plot_width (plot width in meters)
• plot_length (plot length in meters)
• field_size (field size in hectares)
• planting_date (Date of Planting in YYYY-MM-DD format)
• harvest_date (Date of Harvest in YYYY-MM-DD format)
• is_a_control (type 1 in this field if the plot is a control, otherwise 0 or leave blank. generally you will have accessions that are controls, so you should indicate the plots that that accession is in as a control.)
• rep_number (replicate number, must be numeric)
• range_number (range number. often synonymous with col_number, must be numeric)
• row_number (row number. if the field is a grid, this represents the y coordinate, numeric, required for field map generation. the top left plot shuold be row 1, column 1)
• col_number (column number. if the field is a grid, this represents the x coordinate. sometimes called range_number, numeric, required for field map generation. the top left plot shuold be row 1, column 1)
• seedlot_name (the seedlot from where the planted seed originated. must exist in the database)
• num_seed_per_plot (number seeds per plot. seed is transferred from seedlot mentioned in seedlot_name. numeric)
• weight_gram_seed_per_plot (weight in gram of seeds in plot. seed is transferred from seedlot mentioned in seedlot name. numeric)

• treatment columns (additional column(s) that specify the name of a treatment (e.g. inoculated, drought, etc). the value for each plot should be 1 if the treatment was applied or empty if not applied.)

• #CHROM (chromosome: An identifier from the reference genome pointing to a contig in the assembly file (cf. the ##assembly line in the header). All entries for a specific CHROM should form a contiguous block within the VCF file. The colon symbol (:) must be absent from all chromosome names to avoid parsing errors when dealing with breakends. (String, no white-space permitted, Required))
• POS (position: The reference position, with the 1st base having position 1. Positions are sorted numerically, in increasing order, within each reference sequence CHROM. It is permitted to have multiple records with the same POS. Telomeres are indicated by using positions 0 or N+1, where N is the length of the corresponding chromosome or contig. (Integer, Required) )
• ID ( identifier: Semi-colon separated list of unique identifiers where available. If this is a dbSNP variant it is encouraged to use the rs number(s). No identifier should be present in more than one data record. If there is no identifier available, then the missing value should be used. (String, no white-space or semi-colons permitted) )
• REF (reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted. The value in the POS field refers to the position of the first base in the String. For simple insertions and deletions in which either the REF or one of the ALT alleles would otherwise be null/empty, the REF and ALT Strings must include the base before the event (which must be reflected in the POS field), unless the event occurs at position 1 on the contig in which case it must include the base after the event; this padding base is not required (although it is permitted) for e.g. complex substitutions or other events where all alleles have at least one base represented in their Strings. If any of the ALT alleles is a symbolic allele then the padding base is required and POS denotes the coordinate of the base preceding the polymorphism. Tools processing VCF files are not required to preserve case in the allele Strings. (String, Required) )
• ALT (alternate base(s): Comma separated list of alternate non-reference alleles. These alleles do not have to be called in any of the samples. Options are base Strings made up of the bases A,C,G,T,N,*, (case insensitive) or a breakend replacement string as described in the section on breakends. The '*' allele is reserved to indicate that the allele is missing due to a upstream deletion. If there are no alternative alleles, then the missing value should be used. Tools processing VCF files are not required to preserve case in the allele String, except for IDs, which are case sensitive. (String; no whitespace, commas, or angle-brackets are permitted in the ID String itself) )
• QUAL (quality: Phred-scaled quality score for the assertion made in ALT. i.e. -10log10 prob(call in ALT is wrong). If ALT is '.' (no variant) then this is -10log10 prob(variant), and if ALT is not '.' this is -10log10 prob(no variant). If unknown, the missing value should be specified. (Numeric) )
• FILTER (filter status: PASS if this position has passed all filters, i.e. a call is made at this position. Otherwise, if the site has not passed all filters, a semicolon-separated list of codes for filters that fail. e.g. "q10;s50" might indicate that at this site the quality is below 10 and the number of samples with data is below 50% of the total number of samples. "0" is reserved and should not be used as a filter String. If filters have not been applied, then this field should be set to the missing value. (String, no white-space or semi-colons permitted) )
• INFO (additional information: (String, no white-space, semi-colons, or equals-signs permitted; commas are permitted only as delimiters for lists of values) INFO fields are encoded as a semicolon-separated series of short keys with optional values in the format: key=data[,data]. Arbitrary keys are permitted, although the following sub-fields are reserved (albeit optional):
• AA : ancestral allele
• AC : allele count in genotypes, for each ALT allele, in the same order as listed
• AF : allele frequency for each ALT allele in the same order as listed: use this when estimated from primary data, not called genotypes
• AN : total number of alleles in called genotypes
• BQ : RMS base quality at this position
• CIGAR : cigar string describing how to align an alternate allele to the reference allele
• DB : dbSNP membership
• DP : combined depth across samples, e.g. DP=154
• END : end position of the variant described in this record (for use with symbolic alleles)
• H2 : membership in hapmap2
• H3 : membership in hapmap3
• MQ : RMS mapping quality, e.g. MQ=52
• MQ0 : Number of MAPQ == 0 reads covering this record
• NS : Number of samples with data
• SB : strand bias at this position
• SOMATIC : indicates that the record is a somatic mutation, for cancer genomics
• VALIDATED : validated by follow-up experiment
• 1000G : membership in 1000 Genomes

The exact format of each INFO sub-field should be specified in the meta-information (as described above). Example for an INFO field: DP=154;MQ=52;H2. Keys without corresponding values are allowed in order to indicate group membership (e.g. H2 indicates the SNP is found in HapMap 2). It is not necessary to list all the properties that a site does. )
• FORMAT (A format field is given specifying the data types and order (colon-separated alphanumeric String). This is followed by one field per sample, with the colon-separated data in this field corresponding to the types specified in the format. The first sub-field must always be the genotype (GT) if it is present. There are no required sub-fields. As with the INFO field, there are several common, reserved keywords that are standards across the community:
  • GT : genotype, encoded as allele values separated by either of / or |. The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1, 1 | 0, or 1/2, etc. For haploid calls, e.g. on Y, male nonpseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1. If a call cannot be made for a sample at a given locus, '.' should be specified for each missing allele in the GT field (for example './.' for a diploid genotype and '.' for haploid genotype). The meanings of the separators are as follows (see the PS field below for more details on incorporating phasing information into the genotypes):
  • / : genotype unphased
  • | : genotype phased
  • DP : read depth at this position for this sample (Integer)
  • FT : sample genotype filter indicating if this genotype was "called" (similar in concept to the FILTER field). Again, use PASS to indicate that all filters have been passed, a semi-colon separated list of codes for filters that fail, or '.' to indicate that filters have not been applied. These values should be described in the metainformation in the same way as FILTERs (String, no white-space or semi-colons permitted)
  • GL : genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields. In presence of the GT field the same ploidy is expected and the canonical order is used; without GT field, diploidy is assumed. If A is the allele in REF and B,C,... are the alleles as ordered in ALT, the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc. For example: GT:GL 0/1:-323.03,-99.29,-802.53 (Floats)
  • GLE : genotype likelihoods of heterogeneous ploidy, used in presence of uncertain copy number. For example: GLE=0:-75.22,1:-223.42,0/0:-323.03,1/0:-99.29,1/1:-802.53 (String)
  • PL : the phred-scaled genotype likelihoods rounded to the closest integer (and otherwise defined precisely as the GL field) (Integers)
  • GP : the phred-scaled genotype posterior probabilities (and otherwise defined precisely as the GL field); intended to store imputed genotype probabilities (Floats)
  • GQ : conditional genotype quality, encoded as a phred quality -10log10 p(genotype call is wrong, conditioned on the site's being variant) (Integer)
  • HQ : haplotype qualities, two comma separated phred qualities (Integers)
  • PS : phase set. A phase set is defined as a set of phased genotypes to which this genotype belongs. Phased genotypes for an individual that are on the same chromosome and have the same PS value are in the same phased set. A phase set specifies multi-marker haplotypes for the phased genotypes in the set. All phased genotypes that do not contain a PS subfield are assumed to belong to the same phased set. If the genotype in the GT field is unphased, the corresponding PS field is ignored. The recommended convention is to use the position of the first variant in the set as the PS identifier (although this is not required). (Non-negative 32-bit Integer)
  • PQ : phasing quality, the phred-scaled probability that alleles are ordered incorrectly in a heterozygote (against all other members in the phase set). We note that we have not yet included the specific measure for precisely defining "phasing quality"; our intention for now is simply to reserve the PQ tag for future use as a measure of phasing quality. (Integer)
  • EC : comma separated list of expected alternate allele counts for each alternate allele in the same order as listed in the ALT field (typically used in association analyses) (Integers)
  • MQ : RMS mapping quality, similar to the version in the INFO field. (Integer)
  
  If any of the fields is missing, it is replaced with the missing value. For example if the FORMAT is GT:GQ:DP:HQ then 0 | 0 : . : 23 : 23, 34 indicates that GQ is missing. Trailing fields can be dropped (with the exception of the GT field, which should always be present if specified in the FORMAT field). )

The header must be:

The SampleName.LabID column should contain the sample name (exported_tissue_sample_name or accession_name) and it must exist in the database already

The header must be:

• marker_name
• forward_primer
• reverse_primer
• annealing_temperature
• product_sizes

• sequence_motif
• sequence_source
• linkage_group

• s01 and s02 are marker names.
• 139, 170, 194 are product sizes generated by marker s01 and 203,229,290 are product sizes generated by marker s02.
• sample_A, sample_B, sample_C are accession names.
• "1" indicates the presence of PCR product.
• "0" indicates the absence of PCR product.

• date (should be YYYY-MM-DD)
• sample_id (the unique identifier for the sample in the well)
• well_A01 (the position of the sample in the plate e.q. A10)
• row (the row position of the sample in the plate e.g. A)
• column (the column position of the sample in the plate e.g. 10)
• source_observation_unit_name (must exist in the database. the identifier of the origin material. in order of most desirable identifier to least desirable identifier that can be used here: tissue sample name, plant name, plot name, accession name. For blank wells, you can write BLANK here and place a 1 in the is_blank column also.)
• tissue_type (must be either leaf, root, or stem)

• ncbi_taxonomy_id (NCBI taxonomy identifier)
• dna_person (the name of the person who prepared the well)
• notes (any additional notes on the well)
• extraction (free-text for the extraction method e.g. CTAB)
• concentration (concentration in ng/ul)
• volume (volume in ul)
• is_blank (indicates if well is blank. write 1 if blank, otherwise leave empty.)
• facility_identifier (if you would like to include facility identifiers in your genotyping plate layout, you can add facility identifiers in the last column with the header "facility_identifier")

• date (should be YYYY-MM-DD)
• plate_id (an identifier for a grouping of plates. called "Genotyping Project Name" in genotyping plate submission form. e.g. NextGenCassava)
• plate_name (the unique name for the individual plate. called "Plate ID" in genotyping plate submission form. e.g. 18DNA00001)
• sample_id (the unique identifier for the sample in the well. e.g. 18DNA00001_A01)
• well_A01 (the position of the sample in the plate in this format A01)
• well_01A (the position of the sample in the plate in this format 01A)
• tissue_id (the identifier of the origin material. in order of most desirable identifier to least desirable identifier that can be used here: tissue sample name, plant name, plot name, accession name. this can also say 'BLANK' to indicate a blank well.)
• dna_person (the name of the person who plated the individual sample. can be any name.)
• tissue_type (must be either leaf, root, or stem)

• notes (any additional notes on the well)
• extraction (free-text for the extraction method e.g. CTAB)
• facility_identifier (if you would like to include facility identifiers in your genotyping plate layout, you can add facility identifiers in the last column with the header "facility_identifier")

• Value (the identifier of the origin material. e.g. 2018MyPlant0001. in order of most desirable identifier to least desirable identifier that can be used here: tissue sample name, plant name, plot name, accession name. This can also say 'exclude' to indicate a BLANK)
• Column (the column position of the sample e.g. 10)
• Row (the row position of the sample e.g. A)
• Identification (free text)
• Person (the name of the person who plated the individual sample. can be any name.)
• Date (should be YYYY-MM-DD)

• Facility Identifier (if you would like to include facility identifiers in your genotyping plate layout, you can add facility identifiers in the last column with the header "Facility Identifier")

• seedlot_name (must be unique)
• accession_name (must exist in the database. the accession_name is the unique identifier for the named genotype)
• operator_name (the name of the person who oversaw the inventory process. can be any name.)
• amount (number of seeds in seedlot. can be provided in conjunction with weight(g). must provide a value for amount or weight(g) or both.)
  AND/OR
  weight(g) (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight(g) or both.)
• box_name (the box name that the seed is located in. can be any name.)

• description (information about why this seedlot is being added)
• quality (status of the seedlot, for example "ok", "moldy", "insect damage" etc.
• source (an alternate source, such as a plot or plant identifier from which the seed was sourced if no specific cross experiment was entered in the database)

• seedlot_name (must be unique)
• cross_unique_id (must exist in the database. a cross_unique_id can represent a cross between accessions e.g. AxB, but a cross can also represent a cross between specific plots in the field if you have this information)
• operator_name (the name of the person who oversaw the inventory process. can be any name.)
• amount (number of seeds in seedlot. can be provided in conjunction with weight(g). must provide a value for amount or weight(g) or both.)
  AND/OR
  weight(g) (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight(g) or both.)
• box_name (the box name that the seed is located in. can be any name.)

• description (information about why this seedlot is being added)
• quality (brief description of quality, e.g., "ok", "moldy", "insect damage", etc)
• source (an alternate source, such as a plot or plant identifier from which the seed was sourced if no specific cross experiment was entered in the database)

• The following fields can take comma-separated values to indicate there are several values for the accession: organization_name, synonym , PUI, accession number, acquisition date, biological status of accession code, country of origin, donor, donor PUI, donor institute, genome_structure, institute code, institute name, introgression_backcross_parent, introgression_chromosome, introgression_end_position_bp, introgression_map_version, introgression_parent, introgression_start_position_bp, location_code, ncbi_taxonomy_id, notes, organization, ploidy_level, released_variety_name, seed source, state, transgenic, type of germplasm storage code, variety

• accession_name (must be unique)
• species_name (must exist in the database)

• population_name (a population is a grouping of accessions. if the population already exists in the database, the accession will be added into it, otherwise, the new population will be created.)
• organization_name (the name(s) of the organization(s) which use this accession e.g. NARO,IITA)
• synonym (an accession can be known by many names including local popular names. a synonym name can be used instead of the accession_name throughout the database; because of this, synonyms must themselves be unique. e.g. accession_synonym1,accession_synonym001)
• PUI (no definition available)
• accession number (no definition available)
• acquisition date (no definition available)
• biological status of accession code (no definition available)
• country of origin (no definition available)
• donor (no definition available)
• donor PUI (no definition available)
• donor institute (no definition available)
• genome_structure (no definition available)
• institute code (no definition available)
• institute name (no definition available)
• introgression_backcross_parent (no definition available)
• introgression_chromosome (no definition available)
• introgression_end_position_bp (no definition available)
• introgression_map_version (no definition available)
• introgression_parent (no definition available)
• introgression_start_position_bp (no definition available)
• location_code (no definition available)
• ncbi_taxonomy_id (no definition available)
• notes (no definition available)
• organization (no definition available)
• ploidy_level (no definition available)
• released_variety_name (no definition available)
• seed source (no definition available)
• state (no definition available)
• transgenic (no definition available)
• type of germplasm storage code (no definition available)
• variety (no definition available)

• cross_unique_id (must NOT exist in the database)
• cross_combination (required in the header, but value for cross combination (e.g. female accession/male accession) may be left blank)
• cross_type (must be one of the following: biparental, self, open, sib, polycross, bulk, bulk_self, bulk_open, or doubled_haploid)
  • cross type descriptions:
  • biparental: An individual plant pollinated by another individual plant.
  • self: A self pollinated individual plant.
  • open: An individual plant pollinated by a group of plants or open pollinated (pollen may be from a group with known or unknown members).
  • backcross: An individual plant pollinated by one of its parents.
  • sib: Mating between individuals that have at least one parent in common. Generally between two individuals within the same plot.
  • polycross: Mating between individual female parent from a population and the corresponding male population.
  • bulk: A group of plants (usually a related family) pollinated by an individual plant.
  • bulk_self: A group of plants (usually a related family) that are self pollinated (each individual selfed, not combined pollen).
  • bulk_open: A group of plants (usually a related family) that are pollinated by another group of plants or open pollinated (pollen may be from a group with known or unknown members).
  • doubled_haploid: Plants derived from doubling the chromosome number of haploid tissue.
female_parent (accession names or population names must exist as uniquenames in the database)
male_parent (required in the header, but value may be left blank for most cross types. Must be specified for biparental, sib, polycross and bulk cross types. When specified, accession names or population names must exist as uniquenames in the database)
female_parent (accession names must exist as uniquenames in the database)
male_parent (required in the header, but value may be left blank for most cross types. Must be specified for biparental, sib, polycross and bulk cross types. When specified, accession or population names must exist as uniquenames in the database)
female_plot (Plot names must exist in the database)
male_plot (Plot names must exist in the database)
female_parent (accession names must exist as uniquenames in the database)
male_parent (required in the header, but value may be left blank for most cross types. Must be specified for biparental, sib, polycross and bulk cross types. When specified, accession or population names must exist as uniquenames in the database)
female_plant (Plant names must exist in the database)
male_plant (Plant names must exist in the database)
female_parent (female parent names must exist as uniquenames in the database, can be accession, plot, plant or population stock type.)
male_parent (required in the header, but value may be left blank for most cross types. Must be specified for biparental, sib, polycross and bulk cross types. When specified, male parent names must exist as uniquenames in the database, can be accession, plot, plant or population stock type.)

• female_focus_trait
• male_focus_trait
• female_source_trial
• male_source_trial

• After cross unique ids are stored in the database, you can add field crossing data (e.g. pollination date, total number of flowers pollinated, total number of fruits set) or progenies to each cross unique id.
• Field crossing data and progenies can be uploaded via links in crossing experiment detail page or can be added directly in each cross detail page.