| Variant ID: vg0919844661 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 19844661 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 295. )
TGTATGGAGTTGGTGAATGTGGTTTTTCCTTCTCCTCGAGTTTGCGTGAATGTGGAAAAACTTTGTGTTGGCATCCCCTTCTTTTAGCCATGTCAATCGC[G/A]
ATCTCTGCCTTTTCTTCGACTTTGCCACTGCTGCCAGCCCCAAAATTCTTAGCTTGAGGTCTTTCCTGAGCTGGTGTTCATCAGCAGTAAGGATCCTATC
GATAGGATCCTTACTGCTGATGAACACCAGCTCAGGAAAGACCTCAAGCTAAGAATTTTGGGGCTGGCAGCAGTGGCAAAGTCGAAGAAAAGGCAGAGAT[C/T]
GCGATTGACATGGCTAAAAGAAGGGGATGCCAACACAAAGTTTTTCCACATTCACGCAAACTCGAGGAGAAGGAAAAACCACATTCACCAACTCCATACA
| 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 | 87.00% | 6.20% | 2.71% | 4.04% | NA |
| All Indica | 2759 | 92.90% | 2.70% | 2.10% | 2.28% | NA |
| All Japonica | 1512 | 83.80% | 14.20% | 1.98% | 0.00% | NA |
| Aus | 269 | 42.80% | 0.00% | 12.64% | 44.61% | NA |
| Indica I | 595 | 99.20% | 0.20% | 0.17% | 0.50% | NA |
| Indica II | 465 | 96.10% | 0.00% | 1.72% | 2.15% | NA |
| Indica III | 913 | 89.30% | 6.20% | 1.97% | 2.52% | NA |
| Indica Intermediate | 786 | 90.50% | 2.20% | 3.94% | 3.44% | NA |
| Temperate Japonica | 767 | 96.60% | 2.20% | 1.17% | 0.00% | NA |
| Tropical Japonica | 504 | 76.20% | 22.40% | 1.39% | 0.00% | NA |
| Japonica Intermediate | 241 | 58.90% | 35.30% | 5.81% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 4.20% | 3.12% | 2.08% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 3.33% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0919844661 | G -> DEL | LOC_Os09g33610.1 | N | frameshift_variant | Average:37.312; most accessible tissue: Minghui63 root, score: 45.031 | N | N | N | N |
| vg0919844661 | G -> A | LOC_Os09g33610.1 | missense_variant ; p.Ser1203Leu; MODERATE | nonsynonymous_codon ; S1203L | Average:37.312; most accessible tissue: Minghui63 root, score: 45.031 | unknown | unknown | DELETERIOUS | 0.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0919844661 | NA | 6.51E-06 | mr1364 | 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 |
| vg0919844661 | 4.21E-06 | 2.19E-07 | mr1745 | 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 |
| vg0919844661 | NA | 5.77E-06 | mr1161_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 |