| Variant ID: vg1002271573 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 2271573 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 68. )
TATGTTAACAGACTCCTGAATAGATGTAACTTTCATCTCCAAATAGACATGTCAAGACCATTCAAAAAGTGACGAGAAATCTCAGATTGTGAATAATTAG[C/T]
ATCACTAGCTGCCAACCCGTGCGTTGCACGGGTTATTTATCACCATCACAAAATATTAAAAATTTAATTATACATTGGCAATTTTATAAAATTACGGCAA
TTGCCGTAATTTTATAAAATTGCCAATGTATAATTAAATTTTTAATATTTTGTGATGGTGATAAATAACCCGTGCAACGCACGGGTTGGCAGCTAGTGAT[G/A]
CTAATTATTCACAATCTGAGATTTCTCGTCACTTTTTGAATGGTCTTGACATGTCTATTTGGAGATGAAAGTTACATCTATTCAGGAGTCTGTTAACATA
| 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 | 37.70% | 4.10% | 0.91% | 57.28% | NA |
| All Indica | 2759 | 11.70% | 7.00% | 1.27% | 79.96% | NA |
| All Japonica | 1512 | 84.70% | 0.10% | 0.07% | 15.21% | NA |
| Aus | 269 | 14.90% | 0.00% | 1.49% | 83.64% | NA |
| Indica I | 595 | 8.70% | 25.90% | 1.18% | 64.20% | NA |
| Indica II | 465 | 3.20% | 0.90% | 0.86% | 95.05% | NA |
| Indica III | 913 | 18.60% | 0.00% | 1.97% | 79.41% | NA |
| Indica Intermediate | 786 | 11.10% | 4.60% | 0.76% | 83.59% | NA |
| Temperate Japonica | 767 | 91.00% | 0.10% | 0.00% | 8.87% | NA |
| Tropical Japonica | 504 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Japonica Intermediate | 241 | 75.90% | 0.00% | 0.41% | 23.65% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 2.08% | 4.17% | NA |
| Intermediate | 90 | 51.10% | 1.10% | 1.11% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1002271573 | C -> T | LOC_Os10g04740.1 | upstream_gene_variant ; 337.0bp to feature; MODIFIER | silent_mutation | Average:8.813; most accessible tissue: Callus, score: 30.334 | N | N | N | N |
| vg1002271573 | C -> T | LOC_Os10g04740-LOC_Os10g04750 | intergenic_region ; MODIFIER | silent_mutation | Average:8.813; most accessible tissue: Callus, score: 30.334 | N | N | N | N |
| vg1002271573 | C -> DEL | N | N | silent_mutation | Average:8.813; most accessible tissue: Callus, score: 30.334 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1002271573 | NA | 2.95E-08 | mr1645_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 |
| vg1002271573 | 4.47E-06 | 1.18E-06 | mr1645_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 |
| vg1002271573 | NA | 8.57E-06 | mr1647_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 |
| vg1002271573 | 2.93E-06 | 2.93E-06 | mr1979_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 |