Nothing Here Yet
Please refer to the Documentation

Nothing Here Yet
Please refer to the Documentation

Nothing Here Yet
Please refer to the Documentation

Trials may be uploaded in an Excel file (.xls or .xlsx)

---

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

Header:
The first row (header) must contain the following:

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	entry_number

Header as a string:

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,entry_number

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

Header:
The first row (header) must contain the following:

plot_name	cross_unique_id	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	entry_number

Header as a string:

plot_name,cross_unique_id,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,entry_number

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

Header:
The first row (header) must contain the following:

plot_name	family_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	entry_number

Header as a string:

plot_name,family_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,entry_number

Required fields:

• 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)

Optional fields:

• plot_name (must be unique across entire database. If not provided in the file, it will be automatically generated as {trial_name}-PLOT_{plot_number}.)
• 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.)
• 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.)
• 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)
• entry_number (a trial-level entry number assigned to the stock. Numeric)

Treatments:

• 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.)

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Only the required fields are necessary to include in the upload template. You may add any additional optional fields. The fields can be in any order.

Multiple Trial Designs:
Header:
The first row (header) must contain the following, which is an expansion of the single trial design header:

trial_name	breeding_program	location	year	transplanting_date	design_type	description	trial_type	trial_stock_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	entry_number

Header as a string:

trial_name,breeding_program,location,year,transplanting_date,design_type,description,trial_type,trial_stock_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,entry_number

Required fields:

• trial_name (Must be unique across entire database. It is often a concatenation of the year, transplanting_date, 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), URDD (Un-Replicated Diagonal Design), 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), stripplot (Strip Plot / Split Block), p-rep (Partially Replicated), Westcott (Westcott Design))
• description (Additional text with any other relevant information about the trial.)
• accession_name OR cross_unique_id OR family_name (The accession, cross, or family 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.)

Additional optional fields:

• plot_name (Must be unique across entire database. If not provided in the file, it will be automatically generated as {trial_name}-PLOT_{plot_number})
• 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)
• trial_stock_type (The type of stocks that are being evaluated in the trial. Can be either 'accession', 'cross', or 'family_name'. When not provided, 'accession' is used as the default)
• 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)
• transplanting_date(The transplanting_date of the trial was conducted. Date 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.)
• 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.)
• 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)
• entry_number (a trial-level entry number assigned to the stock. Numeric)

Treatments:

• 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.)

---

Header:
The first row (header) should contain the following:

trial_name	breeding_program	location	year	transplanting_date	planting_date	harvest_date	design_type	description	trial_type	plot_width	plot_length	field_size

Required Fields:

• trial_name: the name of the trial (must already exist in the database)

Optional values:

• new_trial_name (A new name for the trial, must not already exist in the database)
• 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.)
• transplanting_date (The transplanting_date of the trial was conducted. Date in YYYY-MM-DD format or 'remove' to remove the date)
• planting_date (Date of Planting in YYYY-MM-DD format or 'remove' to remove the date)
• harvest_date (Date of Harvest in YYYY-MM-DD format or 'remove' to remove the date)
• 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), URDD (Un-Replicated Diagonal Design), 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.)
• 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)

1. Intro
2. Trial Information
3. Design Information
4. Trial Linkage
5. Field Map Information
6. Custom Plot Naming
7. Review Designed Trial

1. This workflow will guide you through designing a new trial in the database

   A field trial represents a field where each plot has a globally unique plot name, a sequential plot number that is unique in the trial (e.g. 101, 102, 103 for three separate plots), and an accession representing the genotype being tested in that plot. In cases where crosses/families are being evaluated (e.g. F1 hybrid, backcrossing), cross unique ids or family names can be used instead of accessions. Each plot can belong to different blocks and reps depending on the experimental design you are using (e.g. complete block vs augmented design). Each plot can have a row number and col number indicating the relative position of the plot in the field.

   To design a trial you need to provide a globally unique trial name. The plot names will be generated based on the trial name you provide (e.g. if the trial name is 2018MyTrial, plot_names will be generated like 2018MyTrial_101, 2018MyTrial_102, etc).

   You also need to provide a list of accessions, cross unique ids or family names to use. Based on the design you have picked, the accessions, cross unique ids or family names will be randomized over the blocks or replicates in the trial.

   You can provide a list of accessions to use as controls or checks in your experiment.

   Depending on the design you have picked, you will need to provide different design parameters (e.g. for complete block you will need to provide number of blocks, while for alpha lattice you will need to provide block size and number of replicates.).

   A trial can represent a yield trial, a phenotyping trial, a crossing block, a greenhouse, a nursery, etc.

   A plot can have many plants, which the database can track as separate entities, allowing you to record plant level observations and information.

   
   
   Go to Next Step

2. Enter basic information about the trial

   Breeding Program:

   ABC-InternationalBiovIntCIATICAR_NRCBIITAKU CLISMABANNARITANARONIHORTTARITOSCI
   Locations: (One or More)

   Cornell BiotechSendusuMbararamitalulakawandaMarukuLyamungo-TaCRIIbadanOnneArushaHoima[Computation]Ibadan-onsiteNIHORT_OnstationKU Main campusAjayi Crowther University Research FarmBabcock University Research FieldNIHORT Off-station Research FieldMurang’aKirinyagaEmbuIkulweNgetta

   No Locations Selected
   Trial Name:

   Location abbreviation will automatically be added as a prefix if multiple locations are selected.

   Trial Type:
   Year:
   Planting Date:
   Plot Width (m):
   Plot Length (m):
   Field Size (ha):
   Plants per Plot:

   Creates plant entries for each plot. Ignore if not adding plant entries.

   Inherits Treatment(s) From Plots:
   Assign row and column data to plants within plots?

   One plant per (row,column) coordinate. Rows and columns will be populated in a zigzag pattern. Row and column numbers start at 1 within each plot.

   Number of rows per plot
   Number of columns per plot

   Description:

   ---

   Stock Type Being Evaluated in Trial:

   Select a stock type accession cross family_name

   ---

   Design Type:

   Usage Help
   Use same randomization for all locations:

   ---

   First validate the form Continue to Next Step

3. Design your trial layout

   Which accessions will be in the field?

   ---

   List of accessions to include (required):

   Which crosses will be in the field?

   ---

   List of crosses to include (required):

   Which family names will be in the field?

   ---

   List of family names to include (required):

   Name of Check 1:

   Name of Check 2:

   List of checks to include (required):

   List of checks to include (required):

   List of checks to include (required):

   List of checks to include. Checks list should be separate from accessions list. (optional):

   List of checks to include. Checks list should be accessions list. (optional):

   List of checks to include. Checks list should be accessions list. (optional):

   List of unreplicated accession (required):

   List of unreplicated cross (required):

   List of unreplicated family_name (required):

   List of replicated accession (required):

   List of replicated cross (required):

   List of replicated family_name (required):

   Need to create a list?    Manage Lists
   Number of rows in design:
   Number of columns in design :
   Number of times replicated accessions are replicated:
   Block sequence:
   Sub-block sequence:
   Default Number of Plants:

   ---

   Number of Plants:

   ---

   Number of Columns (required):

   ---

   Number of columns between two check columns (Optional):
   Number of replicates (required):

   Number of blocks:

   Number of field rows (Required):

   Number of Columns (Required):

   Number of Columns per Block (2 or 4):

   Number of Rows Per Block (Optional):

   Subplot 1 Treatment Name:

   Subplot 2 Treatment Name:

   Subplot 3 Treatment Name:

   Subplot 4 Treatment Name:

   Add Another Treatment:

   + Treatment

   Number of Plants Per Treatment (required):

   ---

   Show optional parameters:

   Column number per block:

   Number of field columns:

   Block size (required):

   Maximum block size (required):

   Which seedlots will you grow in the field?
   This is optional and can be decided later. If you do not know exactly which seedlot packets you will be planting at this time, you can add this information on the Trial Detail Page after the trial has been saved in the database.

   ---

   List of seedlots for selected accessions (optional):

   Number of seeds per plot (required if seedlot list given):

   Need a list of seedlots for the selected accessions?    Search Seedlots for Accessions
   
   Continue to Next Step

4. Is your trial linked with other field trials, genotyping plates, or crossing experiments in the database? If you are unsure, you can skip this. This information can be added from the trial detail page after the trial is saved.

   
   
   Is this trial following-up a previous field trial?:

   No Yes

   Select the trial(s) which preceded this trial:

   If you go on to collect tissue samples for creating a 96 well plate for genotyping, when adding the genotyping plate (96 well plate layout) to the database you can use plot names or plant names or tissue sample names from this field trial. By doing so, we can create linkage between this field trial and the genotyping plate.

   Will this trial be genotyped?:

   No Yes

   If you go on to perform crosses on this field trial, each cross can be linked to specific female and male plots. When you upload these crosses we can then automatically link this field trial to the crossing experiment in the database.

   Will crosses be done on this trial?:

   No Yes
   
   Continue to Next Step

5. Specify the number of rows and columns for the entire field

   By default field map display is set to serpentine and uses the block or rep number as row number.

   If you do not want to create field map along with this trial, set 'Plot layout format' to 'select plot layout format'.

   If you do not know exactly in which rows and columns you will end up planting the plots, do not provide this and go to the next step.

   If you will plant your plots in an irregular (non-rectangular) layout, do not provide this and go to the next step.

   You can upload the exact row and column information for your plots (in any layout shape) on the Trial Detail Page after you have created the trial in the database and actually planted the experiment.

   ---

   Field map display:

   (comes with design)
   Field map display:
   Number of rows (required):

   Plot layout format:

   select plot layout format Zigzag(unserpentine) Serpentine
   
   Continue to Next Step

6. If you want to change the way in which plot names will be generated by the database

   It is recommended to allow the database to create the plot prefixes, so leave the prefix blank unless necessary.

   Custom plot naming/numbering:
    

   block based plot numbers (increment leading digit for every block)

     consecutive plot numbers throughout the blocks

   Plot prefix:

   Plot start number:

   1 101 1001

   Plot number increment:
   
   Continue to Next Step

7. Review the generated trial layout. Make sure to click Submit at the bottom of this page if you approve of the trial!

   Check to confirm that your design looks good. If there are any problems you can redo the randomization step.

   
     

   • Even Block Numbers (e.g. 2,4,...)
   • Odd Block Numbers (e.g. 1,3,...)
   • Checks
   • Odd Rep Numbers (e.g. 1,3,...)
   • Even Rep Numbers (e.g. 2,4,...)

   No field map to display...
   
   Redo Randomization

   ---

   Trial Is Valid
   The following trial will be added

   ---

   
   Add Treatment(s) to Design Confirm (Saves Trial In Database)

Complete! Your trial was saved in the database.

The trial was saved successfully

• You may want to proceed to the trial detail page for the trial you just created.
• You can print barcodes for the plots or plants or tissue samples in this trial.
• You an add phenotypes for the plots or plants in this trial now.

The trial was saved to the database with no errors! Congrats Click Here

Complete! Your trial was saved in the database.

The trial was saved successfully

• You may want to proceed to the trial detail page for the trial you just created.
• You can print barcodes for the plots or plants or tissue samples in this trial.
• You an add phenotypes for the plots or plants in this trial now.

The trial was saved to the database with no errors! Congrats Click Here

This is for uploading VCF genotype data.
VCF is a tab separated format. If your VCF is very large (greater than 10GB), please consider converting it to an HDF5 (.h5) file using Tassel, and uploading the HDF5 formatted file instead.
Header:
The first row (header) must contain the following fields, followed by all genotyped sample names:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample names...

Required fields:

• #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). )

This is for uploading Intertek genotype data.
Please use csv formatted files

For Intertek SNP Result Grid File:

The header must be:

SampleName.LabID	All Marker Names In Separate Columns (e.g. marker name = S12_7926132)

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

For Intertek SNP Information File:

The header must be:

IntertekSNPID	CustomerSNPID	Reference	Alternate	Chromosome	Position	Optional: additional marker info can be included. Please see below.

Optional columns: You can include additional marker infomation by selecting one or more column headers listed below. Please add the selected column(s) after "Position" column.

• Quality
• Filter
• Info
• Format
• Sequence

This is for uploading Tassel HDF5 genotype data.
Please use HDF5 (.h5) formatted files that work with Tassel
Uploading an HDF5 file is important when the size of the VCF grows greater than 10GB

SSR marker info may be uploaded in an Excel file (.xls or .xlsx)
Header:
The first row (header) must contain the following fields:

marker_name	forward_primer	reverse_primer	annealing_temperature	product_sizes	sequence_motif	sequence_source	linkage_group

Required columns:

• marker_name
• forward_primer
• reverse_primer
• annealing_temperature
• product_sizes

Optional columns (required in the header, but value may be left blank)

• sequence_motif
• sequence_source
• linkage_group

SSR data may be uploaded in an Excel file (.xls or .xlsx)
Example of SSR Data Spreadsheet:

sample_name	s01	s01	s01	s02	s02	s02
	139	170	194	203	229	290
sample_A	1	0	0	0	1	1
sample_B	0	0	0	1	0	0
sample_C	0	1	1	0	1	0

Column Info:

• 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.

This is for uploading KASP genotype data.
Please use csv formatted files

For KASP Marker Information File:

The header must be:

MarkerName	Xallele	Yallele	Chromosome	Position	Optional: additional marker info can be included. Please see below.

Note: For dosage calculation, Xallele is used as reference allele (0) and Yallele is used as alternative allele (1).
Optional columns: You can include additional marker information by selecting one or more column headers listed below. Please add the selected column(s) after "Position" column.

• Quality
• Filter
• Info
• Format
• Sequence
• FacilityMarkerName: if you are uploading genotyping data by using facility marker names, please include these names in the KASP marker information file using "FacilityMarkerName" header

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For KASP Result File:
Note: If your genotyping facility assigned facility marker names and facility sample names for the genotyping data generated, you have an option to directly use these facility names for uploading. After uploaded into database, the genotyping data will be automatically linked to the original marker names and sample names.

If you are uploading genotyping data using your marker names and sample names, the header must be:

MarkerName

SampleName

SNPcall

Xvalue

Yvalue

Required columns:

• MarkerName: Must exist in the marker information file. If you are uploading genotyping data using previously stored protocol, marker names must exist in the selected protocol.
• SampleName: Must exist in the database as uniquenames.
• SNPcall: Allele separated by ":" (for example A:G).
• Xvalue: raw data of X.
• Yvalue: raw data of Y.

If you are uploading genotyping data using facility marker names and facility sample names, the header must be:

FacilityMarkerName	FacilitySampleName	SNPcall	Xvalue	Yvalue

Required columns:

• FacilityMarkerName: Must exist in the marker information file.
• FacilitySampleName: Must exist in the database. You can create a link between each sample name and facility sample name by including facility sample name during uploading genotyping plates
• SNPcall: Allele separated by ":" (for example A:G).
• Xvalue: raw data of X.
• Yvalue: raw data of Y.

This is for uploading a pre-existing genotyping plate layout.
File must be Excel file (.xls or .xlsx)
Header:
The first row (header) must contain the following:

date	sample_id	well_A01	row	column	source_observation_unit_name	ncbi_taxonomy_id	dna_person	notes	tissue_type	extraction	concentration	volume	is_blank

Optional column: In addition to sample ids, you can add facility identifiers in the last column with the header: "facility_identifier".

Required fields:

• 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, stem, seed, fruit or tuber)

Optional fields:

• 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")

This is for uploading a Default Coordinate Android Application exported plate layout.
File must be a CSV file (.csv)
(Excel format not supported)

Header:
The first row (header) must contain the following:

date	plate_id	plate_name	sample_id	well_A01	well_01A	tissue_id	dna_person	notes	tissue_type	extraction

Optional column: In addition to sample ids, you can add facility identifiers in the last column with the header: "facility_identifier".

Required fields:

• 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)

Optional fields:

• 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")

This is for uploading a Custom Coordinate Android Application exported plate layout.
File must be a CSV file (.csv)
(Excel format not supported)

Header:
Note that tissue type will be set to 'leaf' if you use this upload type, since tissue type is not provided in the upload and tissue type is required for DaRT.

The first row (header) must contain the following:

Value	Column	Row	Identification	Person	Date

Optional column: In addition to sample ids, you can add facility identifiers in the last column with the header: "Facility Identifier".

Required fields:

• 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)

Optional field:

• 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")

Header:
The first row (header) should contain the following:

seedlot_name	accession_name	operator_name	amount	weight_gram	description	box_name	quality	source

Required fields:

• 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 materials in seedlot. can be provided in conjunction with weight_gram. must provide a value for amount or weight_gram or both.)
  AND/OR
  weight_gram (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight_gram or both.)
• box_name (the box name that the plant material is located in. can be any name.)

Optional fields:

• 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, subplot, or plant identifier from which the seed was collected)

Header:
The first row (header) should contain the following:

seedlot_name	cross_unique_id	operator_name	amount	weight_gram	description	box_name	quality

Required fields:

• 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 materials in seedlot. can be provided in conjunction with weight_gram. must provide a value for amount or weight_gram or both.)
  AND/OR
  weight_gram (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight_gram or both.)
• box_name (the box name that the plant material is located in. can be any name.)

Optional fields:

• description (information about why this seedlot is being added)
• quality (brief description of quality, e.g., "ok", "moldy", "insect damage", etc)

Header:
The first row (header) must contain the accession_name and species_name columns. Additional information can be included by selecting optional column(s) (see below). :

accession_name	species_name	population_name	synonym	description	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	number_of_insertions	organization	ploidy_level	released_variety_name	seed source	state	transgenic	type of germplasm storage code	variety

Comma Separated Fields:

• 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, number_of_insertions, organization, ploidy_level, released_variety_name, seed source, state, transgenic, type of germplasm storage code, variety

Required Fields:

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

Optional Fields:

• description - a free text description of the stock.
• population_name (a population is a grouping of accessions. If the population already exists in the database, the accession will be added to it; otherwise, a new population will be created). Multiple populations can be specified, using the pipe symbol (|) as the separator (for example, pop1|pop2|pop3)
• 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)
• number_of_insertions (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)

Accessions were found with similar names.

The following accessions already exist in the database:

Header:
To set up crosses in the database, please provide required information. The first row (header) must contain the following:

cross_unique_id

cross_combination

cross_type

female_parent

male_parent

Required columns:

• 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, backcross, bulk, bulk_open, bulk_self, doubled_haploid, dihaploid_induction)
• 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 (between a female population and a male accession).
• bulk_open: A group of plants (usually a related family) that are pollinated by another group of plants or open pollinated (between a female population and a male population or unknown male parent).
• bulk_self: A group of plants (usually a related family) that are self pollinated (each individual selfed, not combined pollen).
• doubled_haploid: Plants derived from doubling the chromosome number of haploid tissue.
• dihaploid_induction: Plants derived from reducing the chromosome set from 4 to 2.
• 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, backcross, 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.

Optional columns (additional parent info): You can add additional parent info after male_plant column by using one or more of these column headers.

• female_focus_trait
• male_focus_trait
• female_source_trial
• male_source_trial

Additional cross information:

• 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.