Table 3.
Haplotypes inferred at each region and the fraction of chromosomes carrying each haplotype
|
|
|
Frequency |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Region |
Haplotype |
AK |
BM |
GR |
LB |
PK |
||||
| 1 | GGTICAC | 0.09 | — | 0.78 | 0.33 | 0.20 | ||||
| AGTICAC | — | 0.83 | 0.10 | 0.25 | 0.08 | |||||
| GGCDTTT | 0.12 | — | 0.10 | — | 0.58 | |||||
| GCTICAC | 0.38 | 0.18 | 0.03 | 0.20 | — | |||||
| GCCDTTT | 0.41 | — | — | — | — | |||||
| 2 | GCTCTTC | — | 0.08 | 0.30 | 0.53 | 0.60 | ||||
| GGTCTTT | 0.12 | — | 0.60 | 0.23 | 0.10 | |||||
| ACATCCT | — | 0.78 | — | — | — | |||||
| ATATCCT | 0.68 | — | — | — | 0.15 | |||||
| ACTCTTC | — | 0.03 | 0.10 | 0.08 | 0.05 | |||||
| 3 | CATITC | 0.65 | 0.28 | 0.73 | 0.50 | 0.80 | ||||
| GGCDGT | 0.24 | 0.73 | 0.28 | 0.28 | 0.20 | |||||
| 4 | CCTTATC | 0.47 | 0.38 | 0.20 | 0.13 | 0.55 | ||||
| CCCGTCT | 0.09 | 0.15 | 0.05 | 0.38 | 0.30 | |||||
| AACGTCT | — | 0.13 | 0.65 | 0.40 | — | |||||
| CCCGACT | 0.26 | — | — | — | 0.15 | |||||
| AATTATC | — | 0.35 | — | — | — | |||||
| 5 | CADCAATAG | 0.09 | 0.45 | 0.15 | 0.28 | 0.60 | ||||
| CAITATCCA | 0.35 | 0.05 | 0.40 | 0.25 | — | |||||
| GGITATCCA | 0.03 | 0.43 | 0.23 | 0.30 | — | |||||
| GGITCTCCA | 0.38 | — | — | — | 0.30 | |||||
| CAITCTCCA | 0.09 | 0.03 | 0.23 | 0.03 | 0.10 | |||||
| 6 | TCGIGCTT | — | 0.55 | — | — | 0.55 | ||||
| CTADATTT | — | 0.33 | 0.40 | 0.28 | — | |||||
| CCGIGCTT | 0.62 | — | — | — | — | |||||
| CTADATCC | 0.12 | — | 0.10 | 0.30 | — | |||||
| CTAIGCTT | 0.06 | — | 0.05 | — | 0.30 | |||||
| CTAIGCTC | — | — | 0.30 | — | 0.08 | |||||
| TCGDATCC | — | — | 0.05 | 0.28 | — | |||||
| CCGIGCCC | 0.18 | 0.10 | — | — | — | |||||
| 7 | GCAAGATTA | — | 0.50 | 0.35 | 0.15 | — | ||||
| GCGGGGCCG | 0.56 | — | — | — | 0.25 | |||||
| AGAGCACTA | — | 0.33 | 0.23 | — | — | |||||
| GCAGGGCCG | 0.06 | — | 0.10 | 0.28 | — | |||||
| AGAGCACCG | — | — | — | 0.03 | 0.35 | |||||
| GCGGGACTA | — | — | — | — | 0.28 | |||||
| AGGGCACCG | — | 0.10 | 0.03 | 0.10 | 0.03 | |||||
| 8 | GIGA | 0.59 | — | 0.40 | 0.75 | 0.70 | ||||
| GDAG | 0.32 | 0.65 | 0.13 | — | 0.08 | |||||
| AIGA | — | — | 0.20 | 0.08 | 0.23 | |||||
| AIGG | — | 0.33 | — | — | — | |||||
| 9 | CCAATGG | 0.53 | 0.33 | 0.30 | 0.28 | 0.55 | ||||
| TATGCTC | — | 0.20 | 0.45 | 0.43 | 0.33 | |||||
| TCTGCGC | 0.18 | — | 0.10 | 0.05 | 0.05 | |||||
| TATGCGC | — | 0.23 | — | 0.10 | — | |||||
| CCTGCGC | — | 0.23 | 0.03 | — | 0.05 | |||||
| CATGCGC | 0.18 | — | 0.05 | 0.08 | — | |||||
| 10 | ADTT | 0.32 | 0.18 | 0.18 | 0.28 | 0.88 | ||||
| ADTG | 0.18 | 0.38 | 0.38 | 0.30 | — | |||||
| GIAT | 0.06 | 0.28 | 0.25 | 0.20 | 0.05 | |||||
|
|
GDAT
|
0.12
|
0.13
|
0.15
|
0.20
|
0.08
|
||||
-
Haplotypes that are observed on <5% of all chromosomes are not shown. Alleles for insertion/deletion polymorphisms are: (I) inserted; (D) deleted sequence. Note that the second marker in region 2 is a triallelic SNP. Haplotypes were inferred for these 10 regions since they contain at least four SNPs of ≥0.2 MAF in all breeds, and the SNPs span a distance of at least 9 kb. (AK) Akita; (BM) Bernese Mountain Dog; (GR) Golden Retriever; (LB) Labrador Retriever; (PK) Pekingese.
