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Genotype Report

LCA48

Closest Genetic Relatives

Relatives (parents, offspring, siblings, cousins) are determined by a genetic relatedness metric (plink v1.9; Purcell et al., 2007).

LCA48 currently has no clones in the Galaxy. It has 65 relatives in the Galaxy.

The list of genetic relatives is ordered in descending relatedness. If a number appears to the right of the variety name, that denotes the number of clones of that variety that are currently in the Phylos Galaxy.

Relatives 65

Population Profile

Population Profile is estimated using the program Admixture (Alexander et al., 2009), which is a model-based method that uses genotype data to infer population structure and assign individuals to populations.

LCA48 has heritage similar to varieties in Berry, with a smaller component of genetic variation similar to varieties in Skunk, Landrace, OG Kush.

The standalone bar depicts the observed heritage of LCA48. The majority color within the reference bars dictates primary subpopulation heritage (Red - Skunk, Blue - OG Kush, Green - Landrace, Purple - Berry, Yellow - Hemp, Orange - CBD). The subpopulation reference bars are generated from all of the representative samples in the Phylos Galaxy. Population structure will continue to evolve as more samples are added to the Galaxy.

Created with Highcharts 7.2.2LCA48SkunkBerryLandraceOG Kush
Galaxy Subpopulation Reference Bars
  • Skunk
  • Hemp
  • Berry
  • Landrace
  • CBD
  • OG Kush

Genetic Novelty

Genetic Novelty scores are based on a density metric which is the density of varieties on the Phylos Galaxy. The proportion of Phylos Galaxy varieties in each of the three density score categories is shown along the horizontal bar. Varieties considered rare are in the 90th percentile of the lowest density scores; uncommon varieties are in the 70th-90th percentile. Locations of varieties are based on a Principal Components Analysis (PCA) (plink v1.9; Purcell et al. 2007).

LCA48 has a Genetic Novelty score of common based on its position in the Phylos Galaxy.

The Phylos Galaxy Genetic Novelty Score is an indicator of how many other varieties in our database have genotypes similar to LCA48. Varieties that have Rare Genetic Novelty Scores have very few surrounding genetically similar varieties in the Phylos Galaxy.

Created with Highcharts 7.2.2CommonUncommonRare

Genetic Variation

Genetic Variation is estimated by the inbreeding coefficient (F) using VCFtools (Danecek P et al., 2011).

LCA48 has a high level of genetic variation indicated by the colored bar.

The barplot shows the frequency of all varieties in the Phylos Galaxy grouped by levels of genetic variation. A low level of genetic variation (homozygous) indicates a stabilized or true breeding line that will produce offspring with consistent physical characteristics (phenotypes); varieties with higher levels of genetic variation (heterozygous) are not true-breeding, and will produce offspring with very different physical characteristics.

Created with Highcharts 7.2.2Low VariationHigh Variation

Genetically Distant Varieties

This insight uses the results of the principal components analysis to plot data. Varieties are chosen using a Furthest Point First (Gonzalez, 1985) algorithm that selects a set of samples that are most divergent from each other. This insight gives a sense of the Galaxy location of divergent varieties and can be used to select a plant for crossing with the focal plant that may generate novel phenotypes.

LCA48 is genetically most different from these varieties: Panama, Palouse Peach, TK677, Super Silver Haze #2, Drivers Lane, Alien Dawg

Highlighted varieties are the most genetically divergent from the submitted sample (diamond marker). This 3D plot is representative of how the varieties are spaced in the Phylos Galaxy. Genetically distant varieties may come from different subpopulations and have different cannabinoid profiles, flavor profiles, and growth characteristics. Crossing two distant varieties may generate offspring with interesting and novel phenotypes.

Created with Highcharts 7.2.2LCA48LCA48PanamaPanamaPalouse PeachPalouse PeachTK677TK677Super Silver Haze #2Super Silver Haze #2Drivers LaneDrivers LaneAlien DawgAlien Dawg

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