| Variant ID: vg0404944968 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4944968 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.29, others allele: 0.00, population size: 45. )
ATCCCGACCAGTTCACTATTCACAAATCGGTTGGGAGGGCAAGGGGGGTAAATTTTTGCTAAAATTTAAGGTAAAAAACACATTATTCTCCATTCATTCT[T/C]
AATATATCGATCATCATATATTTTTCTTCGTATGTTGTTGATTTCAGATGGATCGTAGATGGATGTACTATGCGCATTGTTCATCTACCGAGTATAGAGA
TCTCTATACTCGGTAGATGAACAATGCGCATAGTACATCCATCTACGATCCATCTGAAATCAACAACATACGAAGAAAAATATATGATGATCGATATATT[A/G]
AGAATGAATGGAGAATAATGTGTTTTTTACCTTAAATTTTAGCAAAAATTTACCCCCCTTGCCCTCCCAACCGATTTGTGAATAGTGAACTGGTCGGGAT
| 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 | 62.60% | 28.40% | 1.52% | 7.49% | NA |
| All Indica | 2759 | 88.50% | 7.60% | 1.56% | 2.32% | NA |
| All Japonica | 1512 | 9.20% | 70.80% | 1.19% | 18.78% | NA |
| Aus | 269 | 95.20% | 3.00% | 1.49% | 0.37% | NA |
| Indica I | 595 | 91.90% | 6.20% | 1.68% | 0.17% | NA |
| Indica II | 465 | 76.60% | 14.20% | 3.01% | 6.24% | NA |
| Indica III | 913 | 95.40% | 3.00% | 0.33% | 1.31% | NA |
| Indica Intermediate | 786 | 85.00% | 10.20% | 2.04% | 2.80% | NA |
| Temperate Japonica | 767 | 1.70% | 88.00% | 0.65% | 9.65% | NA |
| Tropical Japonica | 504 | 20.40% | 53.80% | 1.39% | 24.40% | NA |
| Japonica Intermediate | 241 | 9.50% | 51.90% | 2.49% | 36.10% | NA |
| VI/Aromatic | 96 | 71.90% | 26.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 56.70% | 32.20% | 5.56% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404944968 | T -> C | LOC_Os04g09320.1 | downstream_gene_variant ; 3734.0bp to feature; MODIFIER | silent_mutation | Average:20.208; most accessible tissue: Callus, score: 49.138 | N | N | N | N |
| vg0404944968 | T -> C | LOC_Os04g09310.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.208; most accessible tissue: Callus, score: 49.138 | N | N | N | N |
| vg0404944968 | T -> DEL | N | N | silent_mutation | Average:20.208; most accessible tissue: Callus, score: 49.138 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0404944968 | 9.10E-06 | NA | mr1022 | 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 |
| vg0404944968 | 1.63E-06 | NA | mr1023 | 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 |
| vg0404944968 | NA | 4.68E-13 | mr1035 | 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 |
| vg0404944968 | 1.65E-06 | NA | mr1079 | 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 |
| vg0404944968 | 8.87E-06 | NA | mr1390 | 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 |