| Variant ID: vg0824611688 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 24611688 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGTCTATCTCACTGCCCCAAGCCTGGTGCTCCTCCTCCAACTGAAGCTGCTGCGCTGTGAGGTCAGTCACCTCGGTCTCTAACTCTCCCACACGCCTCTG[C/A]
TGGTCGTCGATCTCTAACAGAGCCTCCTCGTAAAAGTCGTCTACTACCTCAGCCCATCGTGACAGTCGGGTCACTATCGGGTTGTAGCAGCAAGGTGTGT
ACACACCTTGCTGCTACAACCCGATAGTGACCCGACTGTCACGATGGGCTGAGGTAGTAGACGACTTTTACGAGGAGGCTCTGTTAGAGATCGACGACCA[G/T]
CAGAGGCGTGTGGGAGAGTTAGAGACCGAGGTGACTGACCTCACAGCGCAGCAGCTTCAGTTGGAGGAGGAGCACCAGGCTTGGGGCAGTGAGATAGACT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.60% | 0.70% | 1.02% | 1.67% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 89.70% | 2.10% | 2.98% | 5.16% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 93.50% | 0.40% | 4.82% | 1.30% | NA |
| Tropical Japonica | 504 | 89.50% | 0.40% | 1.19% | 8.93% | NA |
| Japonica Intermediate | 241 | 78.40% | 11.20% | 0.83% | 9.54% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0824611688 | C -> A | LOC_Os08g38940.1 | missense_variant ; p.Gln142His; MODERATE | nonsynonymous_codon ; Q142H | Average:56.542; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | unknown | unknown | TOLERATED | 0.21 |
| vg0824611688 | C -> DEL | LOC_Os08g38940.1 | N | frameshift_variant | Average:56.542; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0824611688 | 3.47E-07 | 1.23E-06 | mr1682 | 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 |
| vg0824611688 | NA | 3.69E-06 | mr1691 | 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 |
| vg0824611688 | NA | 1.01E-07 | mr1693 | 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 |