| Variant ID: vg0808451668 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 8451668 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.77, T: 0.23, others allele: 0.00, population size: 88. )
GAATTGTCAGGTAATAACCCTACATCCTGTTGGCCGGAGCCGGAGTTGCTTTTTATTCACCATAATCACACCAGTACAATATGTGGGGTAGCCTATCTAA[T/C]
TGTTGTCGACATGGCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGCCTTCCTCCTTAAATCCGTGTCCGGCGAGATCAGAGATAGCGCTTTCG
CGAAAGCGCTATCTCTGATCTCGCCGGACACGGATTTAAGGAGGAAGGCTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGCCATGTCGACAACA[A/G]
TTAGATAGGCTACCCCACATATTGTACTGGTGTGATTATGGTGAATAAAAAGCAACTCCGGCTCCGGCCAACAGGATGTAGGGTTATTACCTGACAATTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.40% | 41.20% | 1.04% | 0.34% | NA |
| All Indica | 2759 | 44.40% | 53.50% | 1.67% | 0.47% | NA |
| All Japonica | 1512 | 89.00% | 10.80% | 0.13% | 0.00% | NA |
| Aus | 269 | 3.00% | 96.30% | 0.00% | 0.74% | NA |
| Indica I | 595 | 58.00% | 41.30% | 0.67% | 0.00% | NA |
| Indica II | 465 | 65.60% | 28.80% | 5.59% | 0.00% | NA |
| Indica III | 913 | 22.70% | 75.20% | 0.99% | 1.10% | NA |
| Indica Intermediate | 786 | 46.70% | 52.00% | 0.89% | 0.38% | NA |
| Temperate Japonica | 767 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 78.20% | 21.40% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 80.90% | 19.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 80.20% | 19.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 33.30% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0808451668 | T -> C | LOC_Os08g14140.1 | missense_variant ; p.Ile83Val; MODERATE | nonsynonymous_codon ; I83V | Average:15.087; most accessible tissue: Minghui63 panicle, score: 20.733 | unknown | unknown | TOLERATED | 1.00 |
| vg0808451668 | T -> DEL | LOC_Os08g14140.1 | N | frameshift_variant | Average:15.087; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0808451668 | 1.42E-06 | 1.42E-06 | mr1894 | 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 |
| vg0808451668 | 8.28E-06 | 8.28E-06 | mr1663_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 |