| Variant ID: vg1212386844 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12386844 |
| 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: 222. )
AACGGTGTTGGATCCAATTATCATGCCAGAAGCTAGTTTTTGCTCTGTCACCAATCGTTATTGTCGTTGCCGCTTGAAAGAGTCTTGTGTCCATCTCATC[G/A]
CAAGGCACATTCATGCCTACCCAGGGTTTATCAACTTCTTTCCACTTGAACCAGAGCCAGCGGAGTTGGAGTGCTCTAGAGAACCTGTCCAGATCCGGTA
TACCGGATCTGGACAGGTTCTCTAGAGCACTCCAACTCCGCTGGCTCTGGTTCAAGTGGAAAGAAGTTGATAAACCCTGGGTAGGCATGAATGTGCCTTG[C/T]
GATGAGATGGACACAAGACTCTTTCAAGCGGCAACGACAATAACGATTGGTGACAGAGCAAAAACTAGCTTCTGGCATGATAATTGGATCCAACACCGTT
| 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 | 75.30% | 1.40% | 13.08% | 10.28% | NA |
| All Indica | 2759 | 82.00% | 1.10% | 10.44% | 6.49% | NA |
| All Japonica | 1512 | 58.70% | 2.10% | 20.24% | 19.05% | NA |
| Aus | 269 | 95.90% | 0.00% | 3.72% | 0.37% | NA |
| Indica I | 595 | 76.80% | 1.00% | 18.15% | 4.03% | NA |
| Indica II | 465 | 77.00% | 1.70% | 11.40% | 9.89% | NA |
| Indica III | 913 | 91.70% | 1.10% | 3.18% | 4.05% | NA |
| Indica Intermediate | 786 | 77.60% | 0.80% | 12.47% | 9.16% | NA |
| Temperate Japonica | 767 | 81.70% | 0.90% | 9.39% | 7.95% | NA |
| Tropical Japonica | 504 | 22.80% | 3.40% | 35.71% | 38.10% | NA |
| Japonica Intermediate | 241 | 60.20% | 2.90% | 22.41% | 14.52% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 8.33% | 8.33% | NA |
| Intermediate | 90 | 78.90% | 3.30% | 6.67% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212386844 | G -> DEL | LOC_Os12g22020.1 | N | frameshift_variant | Average:26.777; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg1212386844 | G -> A | LOC_Os12g22020.1 | missense_variant ; p.Ala109Thr; MODERATE | nonsynonymous_codon ; A109T | Average:26.777; most accessible tissue: Minghui63 panicle, score: 42.799 | unknown | unknown | TOLERATED | 0.17 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1212386844 | 1.33E-06 | 4.08E-09 | mr1057 | 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 |
| vg1212386844 | NA | 7.81E-06 | mr1057 | 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 |
| vg1212386844 | 4.19E-07 | NA | mr1156 | 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 |
| vg1212386844 | 1.11E-06 | 7.76E-07 | mr1173 | 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 |
| vg1212386844 | 3.99E-06 | 3.99E-06 | mr1381 | 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 |