| Variant ID: vg0709322081 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 9322081 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 63. )
CTATCCTGGTCATGTACAACTCGGCGAGCTTGGCACCGCTATAATTTGTCTTGACGGGAATGAACCTCGCCGTCTTGGTAAGTCGATCCACGATCACCCA[A/G]
ATGGAATCATACCCCGTTGCGGTCTTGGTTAATCCAACAATAAAATCCATACCTATCTCATCTCATTTCCACTCGGGAATCTTAAGGGGTTGCAGCAAAC
GTTTGCTGCAACCCCTTAAGATTCCCGAGTGGAAATGAGATGAGATAGGTATGGATTTTATTGTTGGATTAACCAAGACCGCAACGGGGTATGATTCCAT[T/C]
TGGGTGATCGTGGATCGACTTACCAAGACGGCGAGGTTCATTCCCGTCAAGACAAATTATAGCGGTGCCAAGCTCGCCGAGTTGTACATGACCAGGATAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.50% | 19.60% | 27.32% | 2.60% | NA |
| All Indica | 2759 | 20.90% | 32.10% | 43.17% | 3.88% | NA |
| All Japonica | 1512 | 97.80% | 0.40% | 1.52% | 0.26% | NA |
| Aus | 269 | 78.40% | 4.80% | 13.38% | 3.35% | NA |
| Indica I | 595 | 10.30% | 45.50% | 42.52% | 1.68% | NA |
| Indica II | 465 | 18.30% | 23.40% | 51.61% | 6.67% | NA |
| Indica III | 913 | 29.20% | 28.80% | 38.34% | 3.61% | NA |
| Indica Intermediate | 786 | 20.70% | 30.80% | 44.27% | 4.20% | NA |
| Temperate Japonica | 767 | 96.60% | 0.40% | 2.61% | 0.39% | NA |
| Tropical Japonica | 504 | 99.20% | 0.40% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 68.80% | 15.60% | 15.62% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 7.80% | 28.89% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0709322081 | A -> DEL | LOC_Os07g16000.1 | N | frameshift_variant | Average:7.872; most accessible tissue: Callus, score: 17.588 | N | N | N | N |
| vg0709322081 | A -> G | LOC_Os07g16000.1 | synonymous_variant ; p.Ile1322Ile; LOW | synonymous_codon | Average:7.872; most accessible tissue: Callus, score: 17.588 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0709322081 | 4.31E-06 | 3.85E-06 | mr1137 | 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 |
| vg0709322081 | NA | 3.17E-06 | mr1246 | 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 |
| vg0709322081 | NA | 3.40E-09 | mr1663 | 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 |