| Variant ID: vg0810864387 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 10864387 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.07, others allele: 0.00, population size: 107. )
TACGATTCGCCATGTGAAAACCTTAACGGCGTAATTGAATTAAGCCGAAACCGAGTCAATCTCATTGGCTCGTTTTTCTCATTGGCGTGCGGTTCCAGTG[G/A]
ACATCTGACTATCCGATGAACACAATCGCGCTCAGCCTTAGTGAGTACTAGACATTCCAGTGAAGTCACCAACACATATACCGATTGATCTCATCAACCC
GGGTTGATGAGATCAATCGGTATATGTGTTGGTGACTTCACTGGAATGTCTAGTACTCACTAAGGCTGAGCGCGATTGTGTTCATCGGATAGTCAGATGT[C/T]
CACTGGAACCGCACGCCAATGAGAAAAACGAGCCAATGAGATTGACTCGGTTTCGGCTTAATTCAATTACGCCGTTAAGGTTTTCACATGGCGAATCGTA
| 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 | 54.90% | 45.00% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 83.70% | 16.20% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 6.70% | 93.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 51.70% | 48.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.30% | 4.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 89.50% | 10.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 70.30% | 29.60% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 87.20% | 12.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 5.00% | 95.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 6.70% | 93.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 12.40% | 87.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 4.20% | 95.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 44.40% | 54.40% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0810864387 | G -> A | LOC_Os08g17750.1 | missense_variant ; p.Pro58Ser; MODERATE | nonsynonymous_codon ; P58S | Average:59.519; most accessible tissue: Minghui63 flag leaf, score: 80.516 | unknown | unknown | DELETERIOUS | 0.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0810864387 | 9.87E-06 | 6.13E-07 | mr1309 | 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 |
| vg0810864387 | NA | 8.86E-06 | mr1401 | 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 |
| vg0810864387 | 8.09E-06 | 5.76E-06 | mr1574 | 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 |
| vg0810864387 | NA | 1.70E-08 | mr1595 | 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 |