| Variant ID: vg0706284147 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 6284147 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GAGCAGGGGCACAAAAAGTTAGGATACCACTCTGAAGTTCTTGCAATGGAAGGCCAAAAATGGTTTTAGTGACAAGGCATTTGGCGATTTATTGAAACTC[A/G]
TCAAGGACATTATTCCGGAGGGAAACAAATTGCCCGAGACAACGTACGAGGCTAAGAAGATAGTCTGCCCTCTATGACTGGAAGTTCAGAAGATTCACGC
GCGTGAATCTTCTGAACTTCCAGTCATAGAGGGCAGACTATCTTCTTAGCCTCGTACGTTGTCTCGGGCAATTTGTTTCCCTCCGGAATAATGTCCTTGA[T/C]
GAGTTTCAATAAATCGCCAAATGCCTTGTCACTAAAACCATTTTTGGCCTTCCATTGCAAGAACTTCAGAGTGGTATCCTAACTTTTTGTGCCCCTGCTC
| 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 | 72.60% | 11.70% | 4.97% | 10.79% | NA |
| All Indica | 2759 | 92.20% | 1.30% | 3.41% | 3.12% | NA |
| All Japonica | 1512 | 41.80% | 33.00% | 7.34% | 17.86% | NA |
| Aus | 269 | 36.40% | 0.00% | 9.29% | 54.28% | NA |
| Indica I | 595 | 89.90% | 2.00% | 5.88% | 2.18% | NA |
| Indica II | 465 | 93.30% | 2.80% | 3.87% | 0.00% | NA |
| Indica III | 913 | 96.20% | 0.30% | 0.55% | 2.96% | NA |
| Indica Intermediate | 786 | 88.50% | 1.00% | 4.58% | 5.85% | NA |
| Temperate Japonica | 767 | 16.00% | 47.20% | 11.21% | 25.55% | NA |
| Tropical Japonica | 504 | 78.60% | 8.10% | 1.98% | 11.31% | NA |
| Japonica Intermediate | 241 | 46.90% | 39.80% | 6.22% | 7.05% | NA |
| VI/Aromatic | 96 | 96.90% | 2.10% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 70.00% | 16.70% | 5.56% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0706284147 | A -> DEL | N | N | silent_mutation | Average:31.384; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 | N | N | N | N |
| vg0706284147 | A -> G | LOC_Os07g11420.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.384; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0706284147 | NA | 4.62E-07 | mr1252 | 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 |
| vg0706284147 | 7.16E-06 | NA | mr1773 | 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 |
| vg0706284147 | 1.65E-06 | 1.65E-06 | mr1994 | 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 |
| vg0706284147 | 9.16E-06 | NA | mr1841_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 |