| Variant ID: vg0816652216 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 16652216 |
| 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: 76. )
ATGATCAGAACATAATTTTGTCTTCATGCTGAGTTGACTAACTATGGAAGCATCTGGTTCAGGAATATGCACTGATGAAGTCAGATCCACCAGTCACTCA[G/A]
CGCCGGTCTCCTCGCCAACACACTGCTCAGGGAGGTGGAGGGCCAACGATCAGACCGGATCCGCAACCTCAGACCTCCAAATCAACTGGTCAGACGGGTC
GACCCGTCTGACCAGTTGATTTGGAGGTCTGAGGTTGCGGATCCGGTCTGATCGTTGGCCCTCCACCTCCCTGAGCAGTGTGTTGGCGAGGAGACCGGCG[C/T]
TGAGTGACTGGTGGATCTGACTTCATCAGTGCATATTCCTGAACCAGATGCTTCCATAGTTAGTCAACTCAGCATGAAGACAAAATTATGTTCTGATCAT
| 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 | 51.20% | 9.30% | 34.77% | 4.78% | NA |
| All Indica | 2759 | 28.50% | 14.80% | 50.92% | 5.84% | NA |
| All Japonica | 1512 | 88.40% | 0.30% | 7.34% | 3.90% | NA |
| Aus | 269 | 77.30% | 3.70% | 18.96% | 0.00% | NA |
| Indica I | 595 | 30.10% | 5.90% | 60.17% | 3.87% | NA |
| Indica II | 465 | 39.80% | 6.20% | 49.89% | 4.09% | NA |
| Indica III | 913 | 18.60% | 27.90% | 46.11% | 7.34% | NA |
| Indica Intermediate | 786 | 32.10% | 11.20% | 50.13% | 6.62% | NA |
| Temperate Japonica | 767 | 91.00% | 0.00% | 2.61% | 6.39% | NA |
| Tropical Japonica | 504 | 85.90% | 0.80% | 13.29% | 0.00% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.40% | 9.96% | 4.15% | NA |
| VI/Aromatic | 96 | 34.40% | 12.50% | 53.12% | 0.00% | NA |
| Intermediate | 90 | 61.10% | 4.40% | 27.78% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0816652216 | G -> A | LOC_Os08g27270.1 | synonymous_variant ; p.Gln308Gln; LOW | synonymous_codon | Average:43.272; most accessible tissue: Minghui63 flag leaf, score: 73.752 | N | N | N | N |
| vg0816652216 | G -> DEL | LOC_Os08g27270.1 | N | frameshift_variant | Average:43.272; most accessible tissue: Minghui63 flag leaf, score: 73.752 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0816652216 | 5.17E-07 | 4.02E-06 | mr1004 | 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 |
| vg0816652216 | 1.74E-07 | NA | mr1005 | 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 |
| vg0816652216 | 8.08E-07 | 5.03E-07 | mr1011 | 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 |
| vg0816652216 | 1.28E-06 | 1.28E-06 | mr1012 | 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 |