| Variant ID: vg0609583002 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9583002 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ACTATAGCAAATTTTGCCAAAAAAAAGTAGTTCTATAGTGAAAATTTATGTGACTTACCCATTAGTATAACCGTGTAGACATATAGAAATGAAATATTTT[C/G]
AGTTTTTTTATCAGAACAAACTATCACTGCTGGTACAAGTTGCTTTTTTGGCCGGTCTAAAATCAGCTATTAAAAATTTTTATTTCTGATTTAATATGAT
ATCATATTAAATCAGAAATAAAAATTTTTAATAGCTGATTTTAGACCGGCCAAAAAAGCAACTTGTACCAGCAGTGATAGTTTGTTCTGATAAAAAAACT[G/C]
AAAATATTTCATTTCTATATGTCTACACGGTTATACTAATGGGTAAGTCACATAAATTTTCACTATAGAACTACTTTTTTTTGGCAAAATTTGCTATAGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.40% | 7.10% | 4.38% | 37.07% | NA |
| All Indica | 2759 | 82.80% | 0.10% | 2.10% | 15.01% | NA |
| All Japonica | 1512 | 6.10% | 21.80% | 7.34% | 64.81% | NA |
| Aus | 269 | 2.60% | 0.00% | 6.69% | 90.71% | NA |
| Indica I | 595 | 85.40% | 0.20% | 1.18% | 13.28% | NA |
| Indica II | 465 | 83.70% | 0.00% | 1.94% | 14.41% | NA |
| Indica III | 913 | 81.90% | 0.00% | 2.30% | 15.77% | NA |
| Indica Intermediate | 786 | 81.30% | 0.30% | 2.67% | 15.78% | NA |
| Temperate Japonica | 767 | 9.50% | 39.60% | 6.13% | 44.72% | NA |
| Tropical Japonica | 504 | 2.20% | 1.20% | 9.13% | 87.50% | NA |
| Japonica Intermediate | 241 | 3.30% | 7.90% | 7.47% | 81.33% | NA |
| VI/Aromatic | 96 | 6.20% | 0.00% | 18.75% | 75.00% | NA |
| Intermediate | 90 | 45.60% | 5.60% | 2.22% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609583002 | C -> G | LOC_Os06g16640-LOC_Os06g16660 | intergenic_region ; MODIFIER | silent_mutation | Average:39.355; most accessible tissue: Callus, score: 57.32 | N | N | N | N |
| vg0609583002 | C -> DEL | N | N | silent_mutation | Average:39.355; most accessible tissue: Callus, score: 57.32 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0609583002 | NA | 1.36E-07 | mr1977 | 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 |
| vg0609583002 | NA | 2.72E-06 | mr1627_2 | Jap_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 |
| vg0609583002 | 1.14E-06 | 3.23E-10 | mr1977_2 | 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 |
| vg0609583002 | NA | 1.34E-06 | mr1977_2 | Jap_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 |