| Variant ID: vg0805513304 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 5513304 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCCAATAGGCATATATCCACGTGCAAAATCAATTTTAGAATTTTCAGAAAAATTCCTCTGAAGCCGGTCTGACCGAGGTACAGTAGCCGGTTTGACCGGG[A/G]
GCCGGTCTGACCGCCTCTGTACCGCCGGTCTGACCGGTGCCCGGTCTGACCGAGGTTGTTCAGCCGGTCTGACCGGTCGCCGGTCTGACCGCGGGACCCA
TGGGTCCCGCGGTCAGACCGGCGACCGGTCAGACCGGCTGAACAACCTCGGTCAGACCGGGCACCGGTCAGACCGGCGGTACAGAGGCGGTCAGACCGGC[T/C]
CCCGGTCAAACCGGCTACTGTACCTCGGTCAGACCGGCTTCAGAGGAATTTTTCTGAAAATTCTAAAATTGATTTTGCACGTGGATATATGCCTATTGGA
| 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 | 43.70% | 36.40% | 16.80% | 3.11% | NA |
| All Indica | 2759 | 64.70% | 12.30% | 21.13% | 1.92% | NA |
| All Japonica | 1512 | 1.80% | 88.50% | 6.75% | 2.98% | NA |
| Aus | 269 | 74.30% | 0.00% | 13.38% | 12.27% | NA |
| Indica I | 595 | 57.60% | 23.50% | 17.65% | 1.18% | NA |
| Indica II | 465 | 54.20% | 15.70% | 27.53% | 2.58% | NA |
| Indica III | 913 | 78.20% | 1.10% | 19.17% | 1.53% | NA |
| Indica Intermediate | 786 | 60.40% | 14.80% | 22.26% | 2.54% | NA |
| Temperate Japonica | 767 | 1.30% | 96.00% | 1.83% | 0.91% | NA |
| Tropical Japonica | 504 | 2.00% | 79.20% | 12.10% | 6.75% | NA |
| Japonica Intermediate | 241 | 2.90% | 84.20% | 11.20% | 1.66% | NA |
| VI/Aromatic | 96 | 22.90% | 7.30% | 56.25% | 13.54% | NA |
| Intermediate | 90 | 34.40% | 41.10% | 21.11% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0805513304 | A -> G | LOC_Os08g09510.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.261; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg0805513304 | A -> DEL | N | N | silent_mutation | Average:38.261; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0805513304 | NA | 9.49E-06 | mr1450 | 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 |
| vg0805513304 | 2.50E-06 | 2.50E-06 | mr1601 | Jap_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 |
| vg0805513304 | NA | 2.93E-09 | mr1866 | 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 |