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F1 Pedigree Test

Where germplasm_type for samples genotyped have been identified as F1, and germplasm_par1 and germplasm_par2 fields have been identified as germplasm_names that match samples in the same dataset, F1 allele match to the identified parents can be calculated.

To calculate F1 match, an expected F1 is first derived which is then compared to the F1 progeny. The expected F1 can only be derived if there is no missing or heterozygous data in either parent. In the case below, only 7 values can be derived for the expected F1.

The ‘par_1 contained’ calculation looks at how many alleles from Parent1 are contained in the SampledF1 ie i.e. how many of marker alleles in the SampledF1 can be explained by the Parent1 contribution. In this case 9/10 of the SampledF1 marker alleles could have been derived from Parent1, so the result is 90% P1_contained.  For the ‘par_2 contained’ calculation, 7/9 of the SampledF1 marker alleles could have been derived from Parent2, so 78% P2_contained.

The calculation of Percent_F1_match is based on the number of marker genotype calls that exactly match between the SampledF1 and the derived F1, as a percent of the total number of markers that are non-missing or non-heterozygous in both parents.  An exact match has to be both alleles matching and so AA and AA are a 100% match, but AA and AT are a zero match

Reproducibility

Pair-wise comparison between all samples with exact matches (case sensitive) for the metadata field names.

For example, samples A,B, and C having the same germplasm_external_code=10001 will have 3 (AB, AC, BC) reproducibility comparisons.

Reproducibility calculations depend on the dataset_type 41222154. For all dataset_types, if there is any missing data (NN or N) in either sample the marker will be ignored in the calculation.

Similarity Matrix

Pair-wise calculation of genotypic similarity amongst among all samples, with sample metadata provided above and left of the matrix. The calculation is displayed as an symmetric matrix (diagonals are a comparison of the same sample and should always = 1) with column names identical to row names.

For example [Table 1]:

In the above table, samples 1 and 2 are very similar, whereas sample 3 is less so; the genetic similarity between samples 1 and 3 is 0.4.

Genetic similarity ranges from 0 (no similarity) to 1 (identical) and is calculated as the average of the comparison scores across all markers

using the following scoring methodology for markers with valid allele calls:

• Dominant: For markers with both samples having a ‘0’ or both samples having a ‘1’, the value is  1 (a match), otherwise the value is 0 (no match)
• Codominant & 2_letter_nucleotide: For markers with both samples having the same  homozygote the value is 1, if one sample is a heterozygote the value is 0.5, or if the samples have different homozygote the value is  0.0. HOW How about both samples being heterozygote? Both samples are the same heterozygote have a value of 1 (note phasing os not considered so AT = the same as TA[2] ).
• SSR: For markers with both samples having the same homozygous allele pair the value is 1, if either sample is a heterozygote the value is 0.5, for different homozygotes the value is 0.

Summary by Markers

Summary Samples Averages

Provides averaged statistics of samples by following sample metadata fields