| Variant ID: vg0722613858 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 22613858 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, C: 0.06, others allele: 0.00, population size: 103. )
CGAGGTGAAGTGGGTGCGCGACCCCGGCGACCCCAGGAGGATGGTGCAGGAGGCCGTCGTCTCGCCGCACTCTCAGGTCTTCAAGCCGCTGCAGTGACTG[A/C]
CTGACCGACCAACCAACCTAAGGTTTGGTTCTTCTGTCACTGAATTTTTTTGTGGCACCGTTGTACAATTGCTCAATGTCGATTAAGGTGTGATTAGCTC
GAGCTAATCACACCTTAATCGACATTGAGCAATTGTACAACGGTGCCACAAAAAAATTCAGTGACAGAAGAACCAAACCTTAGGTTGGTTGGTCGGTCAG[T/G]
CAGTCACTGCAGCGGCTTGAAGACCTGAGAGTGCGGCGAGACGACGGCCTCCTGCACCATCCTCCTGGGGTCGCCGGGGTCGCGCACCCACTTCACCTCG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.30% | 23.10% | 14.77% | 37.77% | NA |
| All Indica | 2759 | 1.90% | 37.40% | 21.78% | 38.89% | NA |
| All Japonica | 1512 | 69.20% | 2.20% | 4.10% | 24.47% | NA |
| Aus | 269 | 1.90% | 5.20% | 5.58% | 87.36% | NA |
| Indica I | 595 | 0.20% | 21.20% | 43.70% | 34.96% | NA |
| Indica II | 465 | 4.90% | 34.60% | 12.26% | 48.17% | NA |
| Indica III | 913 | 1.80% | 54.20% | 11.17% | 32.86% | NA |
| Indica Intermediate | 786 | 1.70% | 31.80% | 23.16% | 43.38% | NA |
| Temperate Japonica | 767 | 80.30% | 1.40% | 5.35% | 12.91% | NA |
| Tropical Japonica | 504 | 47.60% | 4.20% | 3.17% | 45.04% | NA |
| Japonica Intermediate | 241 | 79.30% | 0.40% | 2.07% | 18.26% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 8.33% | 75.00% | NA |
| Intermediate | 90 | 32.20% | 15.60% | 13.33% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0722613858 | A -> DEL | N | N | silent_mutation | Average:17.528; most accessible tissue: Minghui63 root, score: 36.81 | N | N | N | N |
| vg0722613858 | A -> C | LOC_Os07g37720.1 | intron_variant ; MODIFIER | silent_mutation | Average:17.528; most accessible tissue: Minghui63 root, score: 36.81 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0722613858 | NA | 1.97E-18 | mr1077 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0722613858 | NA | 4.56E-42 | mr1124 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0722613858 | NA | 7.10E-13 | mr1441 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0722613858 | NA | 4.11E-09 | mr1595 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0722613858 | 3.28E-06 | 3.47E-07 | mr1509_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |