| Variant ID: vg0907577141 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 7577141 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGTGGCCGAAGATGGAGGAGCACCATTCGCTTCCACATGTGCGCCATCACAACCGCCTTCGGCCCCCGCCACCTCTCTGCAAGTGCCGAACGCGGCCGAC[A/G]
TGGCGAAGGCGGCTGCGGTGGCAAGGGCACTCCAGACCAGGGCGAAGATCCTTTCGACAAGCCAACTGGTGGTGCCCCAAGCCGCTCCATCGCAGCCGGC
GCCGGCTGCGATGGAGCGGCTTGGGGCACCACCAGTTGGCTTGTCGAAAGGATCTTCGCCCTGGTCTGGAGTGCCCTTGCCACCGCAGCCGCCTTCGCCA[T/C]
GTCGGCCGCGTTCGGCACTTGCAGAGAGGTGGCGGGGGCCGAAGGCGGTTGTGATGGCGCACATGTGGAAGCGAATGGTGCTCCTCCATCTTCGGCCACG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.10% | 1.20% | 1.99% | 0.70% | NA |
| All Indica | 2759 | 95.60% | 1.60% | 2.83% | 0.00% | NA |
| All Japonica | 1512 | 96.30% | 0.70% | 0.86% | 2.18% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.10% | 0.80% | 2.02% | 0.00% | NA |
| Indica II | 465 | 95.50% | 1.70% | 2.80% | 0.00% | NA |
| Indica III | 913 | 94.90% | 2.20% | 2.96% | 0.00% | NA |
| Indica Intermediate | 786 | 95.40% | 1.30% | 3.31% | 0.00% | NA |
| Temperate Japonica | 767 | 94.00% | 1.00% | 0.78% | 4.17% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 2.20% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0907577141 | A -> G | LOC_Os09g13150.1 | missense_variant ; p.Met46Val; MODERATE | nonsynonymous_codon ; M46V | Average:22.42; most accessible tissue: Minghui63 young leaf, score: 39.381 | unknown | unknown | TOLERATED | 1.00 |
| vg0907577141 | A -> DEL | LOC_Os09g13150.1 | N | frameshift_variant | Average:22.42; most accessible tissue: Minghui63 young leaf, score: 39.381 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0907577141 | 7.56E-07 | 7.56E-07 | mr1025 | 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 |
| vg0907577141 | 5.89E-06 | 8.43E-06 | mr1208 | Ind_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 |
| vg0907577141 | 4.87E-06 | 4.87E-06 | mr1828 | 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 |