| Variant ID: vg0806335787 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 6335787 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 113. )
ATATTACAAGATTCATCTTTTAAAGTACTTTTATGTGAAGCTAATTTCATATTTGTTGGGAACATAACATAAAATAAATTAATGGTCAAAGTATGTCATT[G/A]
AAGACCGTGTAAAAAAATATTGGCCTTATAATTTGGGACGGAGGGAGTACTAGCGCACAGTTTGGCATATCTTTTAGTTTATAATCGGTCTTCAGTTTGG
CCAAACTGAAGACCGATTATAAACTAAAAGATATGCCAAACTGTGCGCTAGTACTCCCTCCGTCCCAAATTATAAGGCCAATATTTTTTTACACGGTCTT[C/T]
AATGACATACTTTGACCATTAATTTATTTTATGTTATGTTCCCAACAAATATGAAATTAGCTTCACATAAAAGTACTTTAAAAGATGAATCTTGTAATAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.20% | 5.70% | 3.96% | 30.07% | NA |
| All Indica | 2759 | 36.00% | 7.40% | 6.49% | 50.16% | NA |
| All Japonica | 1512 | 98.60% | 0.30% | 0.20% | 0.86% | NA |
| Aus | 269 | 77.30% | 21.60% | 0.00% | 1.12% | NA |
| Indica I | 595 | 28.10% | 0.00% | 7.23% | 64.71% | NA |
| Indica II | 465 | 23.70% | 31.20% | 5.38% | 39.78% | NA |
| Indica III | 913 | 40.70% | 0.30% | 7.34% | 51.59% | NA |
| Indica Intermediate | 786 | 43.60% | 7.10% | 5.60% | 43.64% | NA |
| Temperate Japonica | 767 | 98.60% | 0.10% | 0.26% | 1.04% | NA |
| Tropical Japonica | 504 | 99.00% | 0.20% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.20% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 3.30% | 4.44% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0806335787 | G -> A | LOC_Os08g10770.1 | downstream_gene_variant ; 1952.0bp to feature; MODIFIER | silent_mutation | Average:35.265; most accessible tissue: Callus, score: 63.167 | N | N | N | N |
| vg0806335787 | G -> A | LOC_Os08g10780.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.265; most accessible tissue: Callus, score: 63.167 | N | N | N | N |
| vg0806335787 | G -> DEL | N | N | silent_mutation | Average:35.265; most accessible tissue: Callus, score: 63.167 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0806335787 | NA | 4.91E-07 | mr1082 | 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 |
| vg0806335787 | 5.07E-07 | 3.65E-07 | mr1083 | 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 |
| vg0806335787 | 3.99E-06 | 3.32E-10 | mr1410 | 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 |
| vg0806335787 | 6.22E-06 | 7.74E-08 | mr1411 | 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 |
| vg0806335787 | NA | 4.58E-06 | mr1425 | 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 |