Sample attributes

User-defined and predefined sample attributes can be viewed in the Samples table in Ion Reporter™ Software. Each column in the Samples table represents a single sample attribute.

A set of default columns is always visible in the table. You can also add attributes to the table. To add more attribute columns to the table, or create a reusable table preference, see Customize the Samples table. After you add more attributes to the table, you can further customize the table with filters that you can use to find the attributes. For more information, see Find samples.

Several sample attributes can be edited in Ion Reporter™ Software. For more information, see Edit a sample, Edit a sample used in an analysis, and Define samples with a CSV file.

Each description indicates which attributes cannot be changed.


Attribute	Description
Default columns—These columns are selected by default when you open the Samples table if no table preferences are applied.
	Selection checkbox—Use to select samples to include in analyses.
	Analyzed sample—Indicates that the sample has already been analyzed.
	Locked sample—Indicates that the sample attributes cannot be edited. After a sample is locked, the sample attributes and the files that make up the sample cannot be edited.
	Transferred sample—Indicates that the sample was transferred to a user in another organization.
Sample	The name of the sample.
Gender	Information about the gender of the sample. Female Male Unknown IMPORTANT! Several analysis workflows in Ion Reporter™ Software (for example, the Ion AmpliSeq™ IDP Trio analysis workflows) are limited when the gender is unknown. The analysis workflows can return unexpected results when the gender is incorrectly specified for a sample.
Sample Type	Information about the type of sample. DNA DNA NTC (No Template Control) Metagenomics RNA RNA NTC (No Template Control) MSI On-Chip Control TNA (Total Nucleic Acid)
Project	A list of one or more project names that have been associated with a sample.
Role	The role in a pair or a group of samples, such as mother, father, proband, or unknown.
Imported By	The user name of the person who imported the sample.
Imported On	The date that the sample was imported.
Available columns—These attributes can be added to the Samples table.
Bacterial Marker Type	Only one bacterial marker type can be associated with each barcode in a sample. The list of available bacterial marker types is divided into two categories: 16S rRNA Gene Target Species
Barcode	The name of the specific barcode in the selected barcode kit. This attribute cannot be changed.
Biopsy Days	The time point post-fertilization at which the sample was taken from an embryo biopsy.
Cancer Type	The type of cancer of the sample.
Cell Num	The cell count of the biopsy material.
Chip ID	The number assigned to the chip. This attribute cannot be changed.
Chip Type	The chip type, such as Ion 550™ Chip. This attribute cannot be changed.
Control Sequencing Kit	The control kit used when preparing the sample. This attribute cannot be changed.
Couple ID	An identifier for use with the Reproductive research application.
Device ID	The number of the sequencing instrument. This attribute cannot be changed.
Embryo ID	The number or name assigned to the embryo.
Instrument	The name of the sequencer. This attribute cannot be changed.
Instrument Type	The type of sequencer, such as Ion GeneStudio™ S5 Sequencer. This attribute cannot be changed.
IR Uploader Version	The software version number for the IonReporterUploader plugin. This attribute cannot be changed.
Library Kit Name	The name of the library kit used to prepare the sample. This attribute cannot be changed.
Mouse Strain	If a mouse sample was used, the strain of the mouse sample. 129/Sv A/J BALB/c C57BL/6 I/St MLR/pr NFS NZB Unknown For use with the T-cell and B-cell receptor sequencing analyses. Samples that use the mouse strain attribute can be added to a user-defined analysis workflow. Available options are based on the most common mouse strains in the IRGT database.
Percentage Cellularity	The percent of tumor cells in the sample. Note: The Percentage Cellularity sample attribute is required for DNA samples. IMPORTANT! Do not change this setting for workflows that are used with the Oncomine™ TagSeq Breast DNA Regions, Oncomine™ TagSeq Lung DNA Regions, and Ion AmpliSeq™ HD assays. These assays are targeted to cell free DNA (cfDNA) and do not estimate tumor cellularity because calls are based on P values and cannot be quantified as a ploidy value.
Plan Name	The name of the Planned Run used in Torrent Suite™ Software. This attribute cannot be changed.
Population	The ethnicity indicator for the sample. If European is selected, the haplotype of a T-Cell receptor is included in the analyses results for an Ion AmpliSeq™ Immune Repertoire Assay Plus—TCRβ assay. You can download a corresponding Haplotype Group Assignment plot. For more information about a TCRB-LR assay, see Immune repertoire analysis results Note: The haplotype assignment compares a query sample against a reference database that is derived from European ethnicity samples. You must therefore select the European population value to assign a haplotype. The haplotype assignment will be blank if other population values are selected. The super populations from the 1000 Genomes Project are available as values. Unknown African Ad Mixed American East Asian European South Asian For information about super populations, see www.1000genomes.org.
Run Date	The date of the sequencing run. This attribute cannot be changed.
Run ID	The number of the sequencing run. This attribute cannot be changed.
Run Name	The name of the Planned Run used in Torrent Suite™ Software. This attribute cannot be changed.
Sample Collection Date	The date that the sample was collected from the biological subject. The Sample Collection Date must precede the Sample Receipt Date.
Sample Receipt Date	The date that the sample was received by the processing laboratory. The Sample Receipt Date must be later than or the same as the Sample Collection Date.
Sample ID	A unique identification code (SampleID) for each barcode in a sample. This helps to track samples or possibly identify misassignment between samples and barcodes in a sequencing run. If you manage samples in an external system (for example, a LIMS), you can use the identifier from that system. This attribute cannot be changed.
Sample Preparation Kit	The name of the sample preparation kit used in Torrent Suite™ Software. This attribute cannot be changed.
Sequencing Kit Name	The name of the sequencing kit used in Torrent Suite™ Software. This attribute cannot be changed.
Sequencing Run Type	This value defines the type of sequencing run, for example, Single End or Paired End. In single-end reading, the sequencer reads a fragment from only one end to the other, generating the sequence of base pairs. In paired-end reading, it starts at one read, finishes this direction at the specified read length, and then starts another round of reading from the opposite end of the fragment. In the software, "FRAGMENT" appears for Single End and "PE" appears for Paired End. This attribute cannot be changed.
Templating Kit Name	The name of the templating kit used in Torrent Suite™ Software. This attribute cannot be changed.
Torrent Suite Hotspot File	The name of the hotspots file used in Torrent Suite™ Software. This attribute cannot be changed.
Torrent Suite Region File	The name of the target regions file used in Torrent Suite™ Software. This attribute cannot be changed.
Torrent Suite Results Name	The name of the Torrent Suite™ Software run report. This attribute cannot be changed.
Torrent Suite Version	The Torrent Suite™ Software version number. This attribute cannot be changed.
Attributes defined by the user.
*	User-defined attributes are denoted with an asterisk (*) in the available columns list. Each user-defined attribute is listed in the Samples table and included in a CSV file of sample attributes.

Gender attribute

The gender attribute is a unique sample attribute that is used in various ways. The gender attribute is used by some analysis workflows in Ion Reporter™ Software, including the Ion AmpliSeq™ Exome trio and Ion AmpliSeq™ IDP trio analysis workflows

Several analysis workflows, such as the Ion AmpliSeq™ IDP trio analysis workflows, are limited when the sample gender is Unknown. These analysis workflows return unexpected results when gender is incorrectly specified. For example, in the Ion AmpliSeq™ IDP trio analysis workflow, when the gender of the proband is not known, variants cannot be assigned in the categories HasMaleMaternalX and HasUnknownX.

Gender can be supplied by the Planned Run in Torrent Suite™ Software. You can also add or change the gender attribute when you import a sample, or edit a sample in Ion Reporter™ Software. For example, if a sample that was transferred from Torrent Suite™ Software to Ion Reporter™ Software does not include the gender attribute or includes an attribute value that is not correct, you can edit the sample to add the gender attribute, or change its value.

To edit the gender attribute, first define new samples from the BAM or VCF data files. Then you can add the correct gender information to the new sample. For more information, see Define samples with one or more BAM files and Define a single VCF file as a sample.

Note: Called Gender is another sample attribute that is calculated for some types of analyses and shown in the analysis results. The Called Gender sample attribute cannot be edited or defined manually. The software calculates Called Gender using an algorithm based on the analysis of sex chromosome data.