Table 2. Estimates of heritability.

Phenotype	${\mathit{h}}_{\mathbf{H}}^2$	${\mathit{h}}_{\mathbf{SNP}}^2$	${\mathit{h}}_{\mathbf{SV}}^2$
			IP	LIS	SS	U	U + LIS
Resistance (resistance to A. laibachii)	0.000 (0.139)	0.258 (0.085)	0.490 (0.335)	0.511 (0.307)	0.000 (NA)	0.673 (0.504)	0.503 (0.314)
RosetteLeafNumber.LongDay (number of leaves in a rosette for plants grown under long daylight	0.228 (0.081)	0.322 (0.076)	0.463 (0.148)	0.456 (0.146)	1.000 (NA)	1.000 (0.377)	0.447 (0.146)
RosetteLeafNumber.ShortDay (number of leaves in a rosette for plants grown under short daylight)	0.038 (0.060)	0.047 (0.062)	0.000 (NA)	0.000 (NA)	0.000 (NA)	0.000 (NA)	0.000 (NA)
Bolting.Bath (bolting time in a greenhouse)	0.426 (0.064)	0.476 (0.048)	0.783 (0.093)	0.783 (0.093)	0.952 (0.047)	0.989 (0.025)	0.785 (0.092)
Days.to.germ. (germination time)	0.220 (0.068)	0.149 (0.063)	0.385 (0.116)	0.357 (0.113)	0.598 (0.165)	0.835 (0.146)	0.365 (0.114)
FieldFT.pl (flowering time in the field)	0.000 (0.068)	0.095 (0.076)	0.000 (0.179)	0.000 (0.130)	0.000 (0.913)	0.000 (NA)	0.000 (0.145)
FieldRD.pl (rosette diameter plasticity)	0.000 (NA)	0.000 (0.063)	0.000 (0.085)	0.000 (0.084)	0.000 (0.239)	0.166 (0.220)	0.000 (0.085)
Leaves.day.28.given.days.to.germ (residuals for number of leaves at day 28 regressed on germination)	0.193 (0.081)	0.299 (0.066)	0.391 (0.146)	0.362 (0.140)	0.836 (0.189)	0.675 (0.272)	0.366 (0.142)
ttl_branch.BATH (total number of branches of plants)	0.106 (0.048)	0.196 (0.054)	0.276 (0.104)	0.275 (0.100)	0.419 (0.193)	0.616 (0.214)	0.279 (0.102)

${\mathit{h}}_{\mathbf{H}}^2$ is haplotype-based heritability. ${\mathit{h}}_{\mathbf{SNP}}^2$ is SNP-based heritability. ${\mathit{h}}_{\mathbf{SV}}^2$is the heritability estimated from structural variant anomaly traits. Numbers in brackets are the standard errors (SEs) of the heritability estimates above. Heritability for excess reads are not reported because the fraction of bins in any individual containing nonzero entries was too small. IP, Improperly-paired; LIS, Large Insert Size; SS, Same Strand; U, Unpaired; U + LIS, Unpaired or Large Insert Size.