| Variant ID: vg0809216172 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9216172 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 241. )
TGGCATTACCAGACTTTTCTAAAGAATTTGTGGTTGAGACAGATGCTAGTGGTACAGGCATTGGGGCAGTCCTGATGCAAGATGGACACCCACTGGCTTT[C/T]
ATTAGTAAGGCTCTCAGTCCCAGATCTCAAGCTATGTCAACTTATGAAAAGGAATGTATAGCTGTTCTGCTGGCAGTGGATAAATGGAGGCAGTATTTGC
GCAAATACTGCCTCCATTTATCCACTGCCAGCAGAACAGCTATACATTCCTTTTCATAAGTTGACATAGCTTGAGATCTGGGACTGAGAGCCTTACTAAT[G/A]
AAAGCCAGTGGGTGTCCATCTTGCATCAGGACTGCCCCAATGCCTGTACCACTAGCATCTGTCTCAACCACAAATTCTTTAGAAAAGTCTGGTAATGCCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.10% | 4.10% | 1.18% | 30.62% | NA |
| All Indica | 2759 | 78.00% | 1.40% | 1.16% | 19.39% | NA |
| All Japonica | 1512 | 45.00% | 0.10% | 1.32% | 53.51% | NA |
| Aus | 269 | 46.10% | 53.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 80.70% | 0.20% | 0.50% | 18.66% | NA |
| Indica II | 465 | 51.20% | 0.60% | 1.29% | 46.88% | NA |
| Indica III | 913 | 93.00% | 0.40% | 1.42% | 5.15% | NA |
| Indica Intermediate | 786 | 74.40% | 4.10% | 1.27% | 20.23% | NA |
| Temperate Japonica | 767 | 61.10% | 0.00% | 1.04% | 37.81% | NA |
| Tropical Japonica | 504 | 24.40% | 0.40% | 1.59% | 73.61% | NA |
| Japonica Intermediate | 241 | 36.90% | 0.00% | 1.66% | 61.41% | NA |
| VI/Aromatic | 96 | 17.70% | 2.10% | 3.12% | 77.08% | NA |
| Intermediate | 90 | 62.20% | 4.40% | 1.11% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0809216172 | C -> T | LOC_Os08g15220.1 | synonymous_variant ; p.Phe755Phe; LOW | synonymous_codon | Average:41.58; most accessible tissue: Minghui63 flag leaf, score: 51.386 | N | N | N | N |
| vg0809216172 | C -> DEL | LOC_Os08g15220.1 | N | frameshift_variant | Average:41.58; most accessible tissue: Minghui63 flag leaf, score: 51.386 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809216172 | NA | 1.12E-15 | mr1612 | 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 |
| vg0809216172 | NA | 1.16E-07 | mr1706 | 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 |
| vg0809216172 | NA | 1.67E-07 | mr1989 | 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 |
| vg0809216172 | NA | 2.05E-08 | mr1612_2 | 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 |
| vg0809216172 | 4.53E-06 | NA | mr1746_2 | 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 |