Table 2. Summary of SNPs using G. max as reference genome.

Gray shading, allopolyploid species.

Species	Accession	% Gmax coverage*	Raw SNPs	Processed SNPs**	Synonymous	Non-synonymous
Glycine canescens	1232	7.2 [65.0]	589,686	453,398 [7.7]	148,321	123,413
Glycine clandestina	1126	6.7 [61.4]	496,746	375,943 [7.5]	115,340	96,562
	1253	7.5 [65.1]	617,543	487,923 [8.3]	143,952	124,920
Glycine dolichocarpa	1134	11.6 [77.4]	1,135,676	965,643 [26.4]	242,556	221,326
	1188	7.4 [65.1]	550,698	423,353 [28.9]	132,471	113,785
	1286	4.5 [45.5]	302,661	224,653 [27.9]	67,187	53,595
	1393	6.7 [62.9]	470,402	367,646 [28.8]	125,339	104,549
	1854	7.8 [65.3]	580,531	471,020 [25.8]	140,911	120,274
Glycine syndetika	1300	7.5 [65.5]	605,556	477,245 [7.8]	147,362	125,041
	2073	6.0 [57.6]	402,798	282,215 [12.6]	91,451	75,333
	2321	8.0 [67.7]	670,121	544,101 [6.3]	166,409	143,612
Glycine tomentella D1	1156	8.6 [69.7]	767,614	621,043 [7.6]	190,778	160,781
	1157	6.2 [56.8]	455,265	328,574 [7.1]	94,377	77,945
	1316	7.2 [62.3]	537,439	412,518 [9.3]	120,056	99,666
Glycine tomentella D3	1364	5.0 [51.8]	335,301	226,697 [7.8]	84,917	65,888
	1366	6.6 [59.7]	481,258	360,327 [7.5]	111,011	90,015
	1403	6.4 [60.8]	476,495	369,661 [6.6]	121,526	99,074
	1820	9.3 [69.6]	803,774	641,145 [6.6]	188,965	161,826
Glycine tomentella T1	1288	6.9 [63.0]	498,900	371,845 [19.6]	121,418	102,548
	1361	5.1 [54.2]	293,339	200,738 [18.4]	75,653	59,378
	1763	7.1 [65.5]	533,041	417,420 [19.4]	140,203	116,465
Glycine tomentella T5	A58_1	7.3 [64.6]	544,331	430,552 [27.3]	135,163	113,781
	1487	7.0 [63.6]	516,755	395,503 [26.8]	128,199	105,647
	1969	7.4 [65.9]	558,920	444,468 [27.5]	146,711	124,933

Notes.

^*Between square brackets the coverage of the G. max transcriptome, including alternative splicings.

^**Square brackets, percentage of heterozygous positions.