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Table 2 Number of SNPs for different Axiom™ SNP categories

From: Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization

SNP category

700 K array

70 K array

PolyHighResolution (PHR)

315,642 (48.4%)

66,616 (93.3%)

CallRateBelowThreshold (CRBT)

80,257 (12.3%)

114 (0.2%)

HomHomResolution (HHR)

2 (0%)

0 (0%)

MonoHighResolution (MHR)

4075 (0.6%)

68 (0.1%)

NoMinorHom (NMH)

32,634 (5%)

663 (0.9%)

Other

137,748 (21.1%)

191 (0.3%)

OffTargetVariant (OTV)

51,981 (8%)

78 (0.1%)

AAvarianceX

3695 (0.6%)

537 (0.8%)

AAvarianceY

3884 (0.6%)

538 (0.8%)

ABvarianceX

3613 (0.6%)

653 (0.9%)

ABvarianceY

8566 (1.3%)

533 (0.7%)

BBvarianceX

4773 (0.7%)

821 (1.1%)

BBvarianceY

5071 (0.8%)

551 (0.8%)

Total

651,941

71,363

  1. SNPs from the Axiom arrays are classified into 13 categories, depending on their metrics. The number of SNPs for each category are shown for the Axiom Pear 700 K Genotyping Array (after call adjustment with a confidence threshold of 0.01) and for the Axiom Pear 70 K Genotyping Array