Table 2.

Filtering criteria for single-nucleotide variant (SNV) data from 138 Miscanthus sinensis genotypes

Filtering criteria	Stringent	Liberal
Qa	15	NA
Min depthb	14	3
Min ave depthc	NA	6
Missing (%)d	10	20
Minor allelese	NA	3
Max |FIS|f	0.25	NA
Min het readsg	0.05	NA
No. of allelesh	2	2
Statistics
No. of loci (Sorg)i	20 127	53 174
Ave MAF (Sorg)j	0.027	0.174
Ave r21 kb (Sorg)k	0.24	0.26
No. of loci (Misc)l	30 755	121 771
Ave MAF (Misc)m	0.031	0.115

^aQ, minimum Phred-like SNV quality score (Li et al., 2008).

^bMin depth, minimum number of reads.

^cMin ave depth, minimum average number of reads across all genotypes.

^dMissing (%), maximum percentage of missing genotype data allowed for a given locus.

^eMinor alleles, minimum number of copies of the minor allele among all genotypes.

^fMax |F_IS|, maximum deviation of observed genotype frequencies from Hardy–Weinberg expectations, F_IS = 1 – H_o/H_e, where H_o and H_e are the observed and expected heterozygosities.

^gMin het reads, minimum proportion of reads supporting the less frequent allele in a heterozygous genotype.

^hNo. of alleles, number of SNV alleles detected.

ⁱNo. of loci (Sorg), number of SNVs that passed all filtering criteria based on alignments to the Sorghum bicolor genome.

^jAve MAF (Sorg), average minor allele frequency for SNVs that passed all filtering criteria based on alignments to the Sorghum bicolor genome.

^kAve r²_1 kb (Sorg), average linkage disequilibrium (r², calculated as genotypic correlation) for pairs of loci with MAF ≥ 0.10 that aligned within 1 kb of one another in the Sorghum bicolor genome.

^lNo. of loci (Misc), number of SNVs that passed all filtering criteria based on alignments to an M. sinensis pseudo-reference.

^mAve MAF (Misc), average minor allele frequency for SNVs that passed all filtering criteria based on alignments to an M. sinensis pseudo-reference.

NA, not applicable.