Table 2.

Alignment statistics of exome capture sequencing reads to the switchgrass Release 0 hard-masked genome

Genotype (cultivar, ecotype)	Ploidy	% Reads mapping	Bases covered	Bases covered (>5x)	Exons with coverage	Introns with coverage	Total no. variants detected
A5 (Alamo, lowland)	4x	49.6	274 919 498	114 379 992	212 723	165 173	259 949
AP13(Alamo, lowland)	4x	53.0	316 696 165	161 214 328	223 107	173 130	137 698
SG5-1 (SG5, lowland)	4x	49.3	258 263 021	107 238 627	209 273	162 970	222 623
W4 (Wabasso, lowland)	4x	44.2	235 259 106	122 862 995	212 101	164 618	291 484
Car1 (Carthage, upland)	8x	46.2	225 884 145	110 555 957	214 679	166 790	569 434
P2 (Pathfinder, upland)	8x	43.0	248 703 345	132 893 273	216 841	167 913	415 583
She2 (Shelter, upland)	8x	45.8	227 248 483	101 204 570	207 331	161 402	327 980
Tr5 (Trailblazer, upland)	8x	42.4	240 573 988	129 138 338	215 064	166 872	393 503
Total			517 152 642	244 127 862	245 219	136 819	1 395 501
Concordant			105 225 303	70 957 952	184 883	104 913	578 078

Bases covered indicates the number of bases of the genome with a depth of coverage of at least one uniquely aligned read, while bases covered >5x indicates the number of bases of the genome with a depth of coverage of at least five reads. Exons and introns with coverage indicate the number of exons and introns with a minimum depth of coverage of one. The switchgrass genome (counting only representative gene models) contains 269 451 exons and 203 573 introns. No. of variants indicates the number of sequence variants identified where the position was covered by at least five reads. For an allele to be called a SNP, the alternate allele needed to be represented by at least two reads, or 5% of the total reads, whichever was greater. Concordant refers to bases and variants where there was coverage in all eight genotypes.