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 |