Table 2. Single nucleotide polymorphisms (SNPs) detected across the apple genome by re-sequencing 27 apple accessions.

Chromosome	Sequence used for SNP detection (bp)	SNPs examined from SoapSNP	SNPs passing “Stage 1” filtering	Average distance between SNPs (bp)	Exonic SNPs
1	36,084,648	556,642	102,825	350	31,678
2	40,172,783	793,583	144,715	277	42,496
3	39,907,579	700,701	134,595	296	36,005
4	25,411,901	474,397	91,212	278	27,540
5	37,603,833	661,644	134,672	279	38,400
6	30,670,413	514,972	97,014	316	29,450
7	31,181,013	546,126	117,652	265	33,155
8	35,800,717	625,020	114,173	313	31,946
9	37,514,065	737,124	146,472	256	41,935
10	38,388,612	687,313	146,102	262	43,522
11	40,097,013	751,789	146,718	273	42,681
12	36,276,268	664,326	121,739	297	35,456
13	39,686,055	720,281	158,912	249	43,699
14	34,156,235	607,215	114,259	298	32,712
15	55,775,419	919,506	159,368	349	46,218
16	23,462,870	421,197	85,530	274	24,357
17	27,122,502	533,920	97,162	279	30,349
Total	609,311,926	10,915,756	2,113,120	288	611,599