| Variant ID: vg0107084067 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 7084067 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, A: 0.10, others allele: 0.00, population size: 277. )
TGGACCTCTCCTCCAACAACCTCTCTGGTACCATACCAAAATTCCTTGCAAATTTCACATACTTGACAGCCTTGAATCTGTCCTTCAATAGGCTAGAAGG[C/A]
CAGATACCAGATGGTGGTGTTTTCTCAAACATTACGCTACAGTCCTTGATCGGGAATGCTGCATTATGCGGTGCTCCACGTCTAGGATTTTCACCATGTC
GACATGGTGAAAATCCTAGACGTGGAGCACCGCATAATGCAGCATTCCCGATCAAGGACTGTAGCGTAATGTTTGAGAAAACACCACCATCTGGTATCTG[G/T]
CCTTCTAGCCTATTGAAGGACAGATTCAAGGCTGTCAAGTATGTGAAATTTGCAAGGAATTTTGGTATGGTACCAGAGAGGTTGTTGGAGGAGAGGTCCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.00% | 29.50% | 0.02% | 0.55% | NA |
| All Indica | 2759 | 50.10% | 48.90% | 0.04% | 0.94% | NA |
| All Japonica | 1512 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 9.90% | 89.70% | 0.00% | 0.34% | NA |
| Indica II | 465 | 82.80% | 16.30% | 0.22% | 0.65% | NA |
| Indica III | 913 | 45.20% | 53.60% | 0.00% | 1.20% | NA |
| Indica Intermediate | 786 | 66.80% | 31.90% | 0.00% | 1.27% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 12.20% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0107084067 | C -> A | LOC_Os01g12790.1 | synonymous_variant ; p.Gly863Gly; LOW | synonymous_codon | Average:62.334; most accessible tissue: Callus, score: 82.025 | N | N | N | N |
| vg0107084067 | C -> DEL | LOC_Os01g12790.1 | N | frameshift_variant | Average:62.334; most accessible tissue: Callus, score: 82.025 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0107084067 | NA | 5.43E-06 | mr1518 | 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 |
| vg0107084067 | NA | 2.94E-07 | mr1676 | 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 |
| vg0107084067 | NA | 2.32E-07 | mr1709 | 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 |
| vg0107084067 | 5.03E-08 | NA | mr1699_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 |
| vg0107084067 | 4.34E-08 | 3.24E-07 | mr1699_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 |
| vg0107084067 | NA | 3.28E-08 | mr1709_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 |