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Genome function is influenced by the three-dimensional organization of chromosomes. Kalhor et al. experimentally detect low-frequency intra- and interchromosomal interactions previously obscured by noise and use these data to model the genome architectures of populations of cells.
Over 90% of human whole-genome sequencing has been performed using instruments from two companies, Illumina and Complete Genomics. Lam et al. sequence the same DNA samples with both instruments and compare their performance for calling insertions, deletions and single-nucleotide variants.
Data filters separate true genetic variants in sequencing data from sequencing errors, but their effectiveness is difficult to assess. Reumers et al. use the genome sequences of monozygotic twins to evaluate the performance of filters individually and in combination, leading to a 290-fold reduction in error rate in calling single-nucleotide variants.
A catalog of genetic variation in a crop species facilitates marker-assisted breeding, gene mapping and analysis of elite traits. Xu et al. resequenced 40 cultivated and 10 wild rice accessions to >15 × coverage, yielding 6.5 million single-nucleotide polymorphisms and 808,000 small insertions and deletions.