Abstract: The technology disclosed relates to determining feasibility of using a reference genome of a non-target species for variant calling a sample of a target species. In particular, the technology disclosed relates to mapping sequenced reads of a sample of a target species to a reference genome of a non-target species to detect a first set of variants in the sequenced reads of the sample of the target species, and mapping the sequenced reads of the sample of the target species to a reference genome of a pseudo-target species to detect a second set of variants in the sequenced reads of the sample of the target species.

Abstract: The technology disclosed relates to variant calling of sequenced reads of a sample of a target species against a reference genome of a pseudo-target species. Low-quality variants are identified as false positive variants that are present in the second set of variants but absent from the first set of variants.

Abstract: The technology disclosed relates to identifying differential selective constraint on a gene-by-gene basis between a target species and one or more non-target species. The disclosed systems and methods can use a population genetics model wherein an average selection coefficient per gene per species is estimated and further applied to estimate selective constraint. The disclosed systems and methods can use a generalized linear mixed model wherein depletion of missense variants per gene per species is estimated and further applied to estimate selective constraint. In some cases, the disclosed systems and methods can use various combinations of the components from the population genetics model or the generalized linear mixed model to identify the intersection of genes classified as having differential selective constraint by numerous approaches for validation purposes.

Abstract: A first reference genome is segmented into a plurality of bins and high-quality sequenced reads are mapped on a bin-by-bin basis to the plurality of bins in the first reference genome, and a second reference genome is segmented into a plurality of bins and high-quality sequenced reads are mapped on a bin-by-bin basis to the plurality of bins in the second reference genome. A best-mapped bin is identified in the second reference genome based on the greatest degree of match between the best-mapped bin in the second reference genome and a corresponding bin in the first reference genome.

Abstract: A system divides an input genotype dataset into a plurality of windows, each including a sequence of SNPs and determines a pair of phased haplotype datasets from the plurality of windows of genotype datasets. For at least one window, a plurality of emission probabilities are determined using one or more CNN models that take phased haplotypes as input and generates emission probabilities as output, where the emission probability corresponds to a probability of observing the pair of phased haplotype datasets within the window given a pair of ethnicity labels. The system then generates a directed acyclic graph that comprises a plurality of node groups and a plurality of edges, wherein the node group corresponding to the particular window comprises a plurality of nodes and each node is associated with one of the emission probabilities. Based on the directed acyclic graph, the system generates information on ethnic origin of the individual.

Abstract: An improved graphical user interface (GUI) for displaying patient health records is described herein. A computing device transmits a query to a server computing device executing an electronic health records application (EHR). The EHR retrieves a computer-readable file for a patient comprising a plurality of file records, the plurality of file records including a file record reflective of a patient encounter with a healthcare worker for a healthcare issue. The EHR transmits data which causes the computing device to present a GUI including a first portion comprising an identity of the healthcare issue and a second portion comprising a treatment plan for the healthcare issue, patient symptoms, and observations made by the healthcare worker during the patient encounter. The first portion is oriented above the second portion such that the healthcare issue can be identified without scrolling through the GUI or refreshing the GUI.