Table 4. Apple Infinium® II array v1 content and evaluation in the Plant & Food Research dataset. The number of attempted SNPs and clusters is indicated per linkage group (LG), as well as their density based on the apple genome assembly in kilobases (Kb) and the ‘Golden Delicious’ genetic map (cM).

	Attempted SNPs on IRSC Apple Infinium II array v1				Array evaluation in the Plant & Food Research dataset
LG	No. of SNPs	No. of clusters	Average physical distance between focal points (kb)	Average genetic distance between focal points (cM)	No. of successful beadtypes	No. of poly-morphic SNPs	% poly-morphic SNPs	No. of poly-morphic SNPs with MAF>0.05	MAF>0.05, 50 GC>0.4, call rate >0.95	No. of poly-morphic clusters	% poly-morphic clusters
1	443	81	443.7	1.10	434	299	68.9	250	180	75	92.6
2	695	113	355.1	0.75	684	519	75.9	436	313	108	95.6
3	499	74	538.3	1.19	487	350	71.9	288	212	72	97.3
4	392	65	388.7	1.00	386	292	75.6	235	201	63	96.9
5	492	82	456.9	1.10	486	360	74.1	308	239	76	92.7
6	351	64	473.2	1.17	340	233	68.5	194	117	63	98.4
7	345	71	438.5	0.83	340	215	63.2	181	129	62	87.3
8	405	68	519.9	1.07	399	276	69.2	229	182	62	91.2
9	490	80	449.2	0.91	477	364	76.3	311	232	76	95.0
10	554	83	446.6	1.12	531	377	71.0	271	224	79	95.2
11	466	80	500.7	0.97	456	322	70.6	277	177	73	91.3
12	469	85	426.5	0.87	459	338	73.6	258	210	81	95.3
13	433	81	489.6	0.94	423	299	70.7	229	178	76	93.8
14	388	72	472.2	1.02	374	266	71.1	215	151	64	88.9
15	629	106	525.6	1.09	621	440	70.9	365	253	101	95.3
16	355	74	316.2	0.76	347	271	78.1	215	158	69	93.2
17	461	76	356.7	0.99	448	333	74.3	231	215	70	92.1
Total	7867	1355	446.2	1.00	7692	5554	72.2	4493	3371	1270	93.7

The Apple Infinium® array was evaluated by screening 1398 progeny in 8 segregating populations and 117 individuals from the Plant & Food Research apple germplasm collection.