| Variant ID: vg0801869183 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1869183 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GACAACCCACTGCCCCCAGCGCTGGGTGTAGAGCTTTCGGTCGTTCCCTGCGTGATGTCCGATGGCCTGAGAGATTCCGACCCGGAACAATAGAGAAGTA[C/T]
GATGGGAGTACTAACCCAGAAGAATTTCTTCAAGTCTACTCCATAGTACTTTACGCTGCCGGAGCAGATGACAACGCATTGGCAAATTATTTGCCGACTG
CAGTCGGCAAATAATTTGCCAATGCGTTGTCATCTGCTCCGGCAGCGTAAAGTACTATGGAGTAGACTTGAAGAAATTCTTCTGGGTTAGTACTCCCATC[G/A]
TACTTCTCTATTGTTCCGGGTCGGAATCTCTCAGGCCATCGGACATCACGCAGGGAACGACCGAAAGCTCTACACCCAGCGCTGGGGGCAGTGGGTTGTC
| 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 | 86.10% | 2.60% | 1.23% | 10.09% | NA |
| All Indica | 2759 | 76.60% | 4.30% | 2.10% | 16.93% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.00% | 0.13% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 74.80% | 0.00% | 2.86% | 22.35% | NA |
| Indica II | 465 | 87.70% | 0.40% | 0.43% | 11.40% | NA |
| Indica III | 913 | 73.90% | 7.00% | 2.30% | 16.76% | NA |
| Indica Intermediate | 786 | 74.60% | 6.90% | 2.29% | 16.28% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 1.10% | 0.00% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0801869183 | C -> T | LOC_Os08g03930.1 | synonymous_variant ; p.Tyr458Tyr; LOW | synonymous_codon | Average:59.381; most accessible tissue: Minghui63 flag leaf, score: 78.782 | N | N | N | N |
| vg0801869183 | C -> DEL | LOC_Os08g03930.1 | N | frameshift_variant | Average:59.381; most accessible tissue: Minghui63 flag leaf, score: 78.782 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0801869183 | NA | 7.02E-06 | Yield | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0801869183 | 2.99E-06 | 1.56E-07 | mr1134_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 |
| vg0801869183 | NA | 2.78E-07 | mr1672_2 | Ind_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 |