Output Description

Build QTL Genotype Probability Data Set

Running this process for the BCSample sample setting generates the following Results window. Refer to the Build QTL Genotype Probability Data Set process description for more information.

Output Data

This process generates the following data set:

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Genotype Probability Output Data Set: This data set contains the genotype probabilities estimated between observed markers along the genetic distance map. It is formatted specifically for internal use with the QTL IM, CIM and MIM Analysis process, where the probabilities are used in the Interval Mapping and Composite Interval Mapping algorithms to find significant QTLs at testing cM intervals. For crosses with 3 distinct possible genotypes (such as an F2), there will be two columns per chromosome and cM interval position, whereas there will be just one column for crosses with only 2 distinct genotypes (for example Backcrosses). The first row contains the chromosome number, the second contains the cM interval, the third contains indicator variables to markers (1 indicates marker and 0 inter-marker position).

The qtlbcsample_geno_gp.sas7bdat output data set lists the probabilities of observing specific QTL genotypes at each one cM interval along the chromosome(s) represented by the markers for each of the 300 individuals listed in the input data set (rows 3 through 302). Row 1 specifies the relevant chromosome, row 2 specifies the interval, and row 3 indicates markers (1 indicates marker and 0 inter-marker position).

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Launch Follow-up Processes

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QTL IM, CIM and MIM Analysis: Click to launch the IM and CIM Analysis (Single QTL Model) process with the input genotype data set, the input annotation data set, and the computed Genotype Probability Data Set preloaded as input.

General

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Click to reopen the completed process dialog used to generate this output.

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Click to close all graphics windows and underlying data sets associated with the output.