Figure 1: A diagram of data generation and data dependencies.
From: Novel sequences, structural variations and gene presence variations of Asian cultivated rice
Raw inputs are displayed in grey boxes and important outputs are shown in blue boxes. Data formats are shown in the brackets. The analysis procedure includes: 1) removal of 14 accessions; 2) selection of 453 high-depth accessions; 3) SV calling for 3,010 accessions against the Nipponbare reference genome and extraction of high-quality SVs for the 453 accessions; 4) construction of the pan-genome sequences by combining the Nipponbare reference genome and non-redundant novel sequences; and 5) determination of presence/absence variation of genes and gene families in the 453 accessions with the “map-to-pan” strategy. Detailed methods are described in the Methods section.
