TABLE 2.

Numbers of different types of SNPs in each sample.

Category	Sample
	132000B-3	827-3	Pool-1	Pool-2
Upstream	198,815	191,492	183,517	184,693
Exonic
Stop gain	1413	1368	1369	1374
Stop loss	312	279	303	296
Synonymous	199,462	185,084	180,793	182,697
Non-synonymous	129,560	127,684	120,964	121,908
Intronic	235,940	225,057	217,002	218,718
Splicing	819	843	783	784
Downstream	169,458	164,570	157,669	158,846
Upstream/downstream	40,394	38,739	36,758	37,111
Intergenic	951,592	982,478	948,986	951,504
ts	1,101,608	1,099,459	1,057,621	1,063,042
tv	826,164	818,142	790,530	794,896
ts/tv	1.333	1.343	1.337	1.337
Total	1,927,772	1,917,601	1,848,151	1,857,938

132000B-3, aberrant parental plant 132000B-3 displaying ectopic blade-like outgrowths on the adaxial side of leaf; 827-3, parental plant with normal leaves; Pool-1, bulked DNA pool for individuals with normal leaves from the F_2:3 family; Pool-2, bulked DNA pool for individuals with ectopic blade-like outgrowths from the F_2:3 family. Upstream, variant overlaps the 1-kb region upstream of the transcription start site; Exonic, variant overlaps a coding exon; Stop gain, an SNP that leads to the immediate creation of stop codon at the variant site; Stop loss, a SNP that leads to the immediate elimination of a stop codon at the variant site; Synonymous, a single-nucleotide variant that does not cause an amino acid change; Non-synonymous, a single-nucleotide variant that cause an amino acid change; Intronic, variant overlaps an intron; Splicing, variant is within 2 bp of a splicing junction; Downstream, variant overlaps the 1-kb region downstream of the transcription end site; Upstream/downstream, variant overlaps the 1-kb region upstream of transcription start site for a gene, while it overlaps the 1-kb region downstream of transcription end site of another gene at the same time; Intergenic, variant is in intergenic region; ts, transition; tv, transversion; ts/tv, the ratio of transition/transversion.