Fig. 2

Evaluation of the assembly strategy by investigating k-mer distributions of reads of the indica accessions and the assembly result with randomly sampled accessions. a Number of k-mers with different depth in total sequencing reads and clean reads. b Proportion of k-mers present in the final assembly for k-mers with differing depth in all the sequencing reads. c Proportion of k-mers present in the final assembly for k-mers that are found in various numbers of accessions. d Number of k-mers with specific depth in reads of randomly sampled accessions. Each sampling was conducted with five replicates. The y-axis, Fold change for number of distinct k-mers, is the number of distinct k-mers in different numbers of sampled accessions divided by that of ten randomly sampled accessions. Vertical bars represent the standard deviation. The red line is the fitting curve determined by regression modeling. e The proportion of k-mers in the indica final assembly recovered by the assembly of randomly sampled rice accessions. The assemblies of 100, 150, and 200 accessions were generated with three replicates while the assemblies of 250 and 300 accessions were generated without replicates. Error bars represent the standard deviation. f The number of contigs and the length of all the contigs for each assembly result. All the assemblies were generated using the approach described in the “Materials and methods”, without the removal of contaminations by aligning to the NCBI Nucleotide collection database