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Table 3 Distributions of SNPs included in the genetic map study grouped by compatible and incompatible classifications

From: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

SNP classification

N

Classification

code

Compatible

No adjustment needed

6417

A

Adjustment needed – type of adjustment

  

Set ambiguous cluster position(s) between cluster groups in Axiom data

821

B

Heterozygous cluster(s) in Axiom data mistakenly grouped with homozygous cluster

737

C

Only 1 to 2 discordant SNP calls

223

D

Malus floribunda 821 specific clustering discordancy between arrays

109

E

Required adjustment to cluster position in Infinium data

37

F

Only issue is rare null alleles that are difficult to identify in Axiom data

27

G

Malus floribunda 821 specific SNP with discordant clustering

26

H

True allele found for null alleles in Infinium data using Axiom data

11

I

Set several SNP calls to missing data and unable to call rare null alleles in Axiom data

4

B/G

Total:

8412

 

Incompatible

Poor cluster differentiation with the Axiom array

808

J

One or more heterozygous cluster overlapping with homozygous cluster in Axiom data

663

K

All clusters overlap, with no clear cluster differentiation in Axiom data

161

L

Inconsistent and irresolvable clustering between platforms

86

M

Extra cluster(s) causing inconsistent clustering and/or illogical co-segregation

78

N

Missing one cluster in Axiom data

51

O

Normal clustering but had more than two unresolvable Mendelian inconsistent errors and/or more than 5 Mendelian consistent errors observed in > 5 unrelated individuals in Axiom data

25

P

Inability to easily identify common null alleles in Axiom data

9

Q

SNP not in Axiom array

2

R

Total:

1883