| Variant ID: vg1217237364 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17237364 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AATTGTTTCTTTGATTCTAGGGCTTCGGTTACAAATTGCCAATTGGTAGTAGGGCCACAGCTTGATCCACAAAAAAGGAATTTTTCTAGCCACATCAGCA[G/A]
AAAGGCTACATGCTCTCGAGGAGTGACGGGCCCTTTACCCATGTATGCTGCTACATAGCCTGACCAACCACCTATGCTCTTGGTCTTGAAGTCGTATTGA
TCAATACGACTTCAAGACCAAGAGCATAGGTGGTTGGTCAGGCTATGTAGCAGCATACATGGGTAAAGGGCCCGTCACTCCTCGAGAGCATGTAGCCTTT[C/T]
TGCTGATGTGGCTAGAAAAATTCCTTTTTTGTGGATCAAGCTGTGGCCCTACTACCAATTGGCAATTTGTAACCGAAGCCCTAGAATCAAAGAAACAATT
| 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 | 82.90% | 10.20% | 1.65% | 5.29% | NA |
| All Indica | 2759 | 73.10% | 17.10% | 1.99% | 7.76% | NA |
| All Japonica | 1512 | 96.20% | 0.30% | 1.19% | 2.25% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 89.70% | 9.10% | 0.50% | 0.67% | NA |
| Indica II | 465 | 67.10% | 27.30% | 1.94% | 3.66% | NA |
| Indica III | 913 | 64.60% | 15.80% | 2.96% | 16.65% | NA |
| Indica Intermediate | 786 | 73.90% | 18.80% | 2.04% | 5.22% | NA |
| Temperate Japonica | 767 | 97.40% | 0.10% | 0.78% | 1.69% | NA |
| Tropical Japonica | 504 | 94.20% | 0.40% | 1.79% | 3.57% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.80% | 1.24% | 1.24% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 3.30% | 5.56% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1217237364 | G -> DEL | LOC_Os12g29120.1 | N | frameshift_variant | Average:38.525; most accessible tissue: Minghui63 flag leaf, score: 79.962 | N | N | N | N |
| vg1217237364 | G -> A | LOC_Os12g29120.1 | synonymous_variant ; p.Leu207Leu; LOW | synonymous_codon | Average:38.525; most accessible tissue: Minghui63 flag leaf, score: 79.962 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217237364 | 3.12E-06 | NA | mr1149 | 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 |
| vg1217237364 | 2.62E-06 | 1.54E-06 | mr1149 | 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 |