| Variant ID: vg0321870751 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 21870751 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 213. )
TGTCACCAGAACAGGCAGTGTTCGAGAAACCCGAGGGGACAGAGAATCGGCATCTTAAACCATTGTATATAAACGGCTACGTCAATGGGAAGCCGATGTC[T/A]
AAGATGATGGTCGATGGTAGGGCCGCGGTAAATTTGATGCCTTATGCCACGTTCAGGAAGTTGGGTAGAAATGCCGAGGATCTCATCAAGACAAATATGG
CCATATTTGTCTTGATGAGATCCTCGGCATTTCTACCCAACTTCCTGAACGTGGCATAAGGCATCAAATTTACCGCGGCCCTACCATCGACCATCATCTT[A/T]
GACATCGGCTTCCCATTGACGTAGCCGTTTATATACAATGGTTTAAGATGCCGATTCTCTGTCCCCTCGGGTTTCTCGAACACTGCCTGTTCTGGTGACA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.00% | 6.40% | 3.87% | 19.72% | NA |
| All Indica | 2759 | 50.80% | 10.70% | 6.42% | 32.04% | NA |
| All Japonica | 1512 | 98.40% | 0.00% | 0.00% | 1.59% | NA |
| Aus | 269 | 94.10% | 0.00% | 1.12% | 4.83% | NA |
| Indica I | 595 | 87.90% | 0.50% | 5.55% | 6.05% | NA |
| Indica II | 465 | 39.40% | 21.70% | 5.59% | 33.33% | NA |
| Indica III | 913 | 34.80% | 10.00% | 5.15% | 50.05% | NA |
| Indica Intermediate | 786 | 48.10% | 12.80% | 9.03% | 30.03% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.40% | 0.00% | 0.00% | 4.56% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 81.10% | 5.60% | 3.33% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0321870751 | T -> A | LOC_Os03g39350.1 | synonymous_variant ; p.Ser762Ser; LOW | synonymous_codon | Average:39.229; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 | N | N | N | N |
| vg0321870751 | T -> DEL | LOC_Os03g39350.1 | N | frameshift_variant | Average:39.229; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0321870751 | NA | 4.87E-07 | mr1425 | 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 |
| vg0321870751 | 2.52E-06 | NA | mr1425_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 |
| vg0321870751 | NA | 7.74E-08 | mr1425_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 |