| Variant ID: vg0900360701 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 360701 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTGACCGGCCCAGGGCCCGGTCTGACCGGCATCATGATGCGCGGTCGGACCGGCCTGAGAGCCGGTCTGACCGCCGGGATAATACCCGGTCTGACCGGCC[G/A]
TCAGGCCCGGTCGGACCGGCCGTGAACGCCGTTCTGTCGGTTTTACTACCCGTTTGACCTATAGGAGGTTGATTAGCAGTGGTATAGGCTTTATCTTTTA
TAAAAGATAAAGCCTATACCACTGCTAATCAACCTCCTATAGGTCAAACGGGTAGTAAAACCGACAGAACGGCGTTCACGGCCGGTCCGACCGGGCCTGA[C/T]
GGCCGGTCAGACCGGGTATTATCCCGGCGGTCAGACCGGCTCTCAGGCCGGTCCGACCGCGCATCATGATGCCGGTCAGACCGGGCCCTGGGCCGGTCAG
| 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 | 67.30% | 2.70% | 23.04% | 7.00% | NA |
| All Indica | 2759 | 62.30% | 4.00% | 30.74% | 2.94% | NA |
| All Japonica | 1512 | 83.00% | 0.00% | 0.66% | 16.34% | NA |
| Aus | 269 | 11.90% | 5.60% | 82.53% | 0.00% | NA |
| Indica I | 595 | 61.50% | 3.70% | 31.09% | 3.70% | NA |
| Indica II | 465 | 67.70% | 2.20% | 28.39% | 1.72% | NA |
| Indica III | 913 | 60.00% | 5.30% | 32.31% | 2.41% | NA |
| Indica Intermediate | 786 | 62.30% | 3.90% | 30.03% | 3.69% | NA |
| Temperate Japonica | 767 | 68.80% | 0.00% | 0.91% | 30.25% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.00% | 0.83% | 5.39% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 6.67% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0900360701 | G -> DEL | LOC_Os09g01490.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0900360701 | G -> A | LOC_Os09g01490.1 | synonymous_variant ; p.Asp149Asp; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0900360701 | NA | 4.17E-07 | mr1680 | 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 |
| vg0900360701 | 3.39E-06 | 3.39E-06 | mr1966 | 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 |