| Variant ID: vg0323605084 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 23605084 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 105. )
ACATCAACCAGTACTAAAGATAGATTTTTACTCCCGGTTATTTCACCCGGGACTAAAGATAGCGATTTTTAGTCTCGGATTCGTAGTCCCGGTTGGAAAA[C/T]
CGGGACTAAAGTGGGGTTACGAATCGAGAGTAAAAACTACTTCTCCACCAGTGTGACAACTCAGCTAAGAGCGTGCCCCAGTTTGGTTTCTCGAGTCCAA
TTGGACTCGAGAAACCAAACTGGGGCACGCTCTTAGCTGAGTTGTCACACTGGTGGAGAAGTAGTTTTTACTCTCGATTCGTAACCCCACTTTAGTCCCG[G/A]
TTTTCCAACCGGGACTACGAATCCGAGACTAAAAATCGCTATCTTTAGTCCCGGGTGAAATAACCGGGAGTAAAAATCTATCTTTAGTACTGGTTGATGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.90% | 45.80% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 80.40% | 19.20% | 0.43% | 0.00% | NA |
| All Japonica | 1512 | 0.80% | 99.10% | 0.13% | 0.00% | NA |
| Aus | 269 | 95.20% | 4.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 67.90% | 31.40% | 0.67% | 0.00% | NA |
| Indica II | 465 | 80.90% | 18.90% | 0.22% | 0.00% | NA |
| Indica III | 913 | 89.00% | 10.50% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 79.50% | 20.10% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 0.30% | 99.60% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 1.20% | 98.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.70% | 98.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 20.80% | 79.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 43.30% | 55.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0323605084 | C -> T | LOC_Os03g42420.1 | upstream_gene_variant ; 4687.0bp to feature; MODIFIER | silent_mutation | Average:58.953; most accessible tissue: Minghui63 young leaf, score: 69.4 | N | N | N | N |
| vg0323605084 | C -> T | LOC_Os03g42410-LOC_Os03g42420 | intergenic_region ; MODIFIER | silent_mutation | Average:58.953; most accessible tissue: Minghui63 young leaf, score: 69.4 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0323605084 | NA | 5.97E-12 | mr1553 | 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 |
| vg0323605084 | NA | 1.06E-08 | mr1322_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 |
| vg0323605084 | NA | 4.02E-17 | mr1553_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 |
| vg0323605084 | NA | 1.13E-06 | mr1553_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 |