| Variant ID: vg0517978444 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 17978444 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCGCCATCGCCAGACTTGGAGCGAGGCGGCTGGTGCCAGACATGGAGCTGGACGAGTGCGCGCGCGGAGCAACGATGGAGAAGCTACTCGCTCCACAGTG[C/T]
GGCTGCGGCGCTCTCTCCCTGCCCCACGTGACCTCGATATCACCGAAGAACTTGTGACCTTCTTTGGACGCGAGGACCTCATGTTGGTGGGTCCAAGCAC
GTGCTTGGACCCACCAACATGAGGTCCTCGCGTCCAAAGAAGGTCACAAGTTCTTCGGTGATATCGAGGTCACGTGGGGCAGGGAGAGAGCGCCGCAGCC[G/A]
CACTGTGGAGCGAGTAGCTTCTCCATCGTTGCTCCGCGCGCGCACTCGTCCAGCTCCATGTCTGGCACCAGCCGCCTCGCTCCAAGTCTGGCGATGGCGC
| 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 | 59.10% | 24.30% | 0.15% | 16.42% | NA |
| All Indica | 2759 | 92.40% | 2.80% | 0.11% | 4.71% | NA |
| All Japonica | 1512 | 9.30% | 48.80% | 0.26% | 41.67% | NA |
| Aus | 269 | 23.00% | 77.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 75.30% | 1.90% | 0.43% | 22.37% | NA |
| Indica III | 913 | 95.20% | 4.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.40% | 2.20% | 0.13% | 3.31% | NA |
| Temperate Japonica | 767 | 3.30% | 76.00% | 0.26% | 20.47% | NA |
| Tropical Japonica | 504 | 20.60% | 18.30% | 0.20% | 60.91% | NA |
| Japonica Intermediate | 241 | 4.60% | 26.10% | 0.41% | 68.88% | NA |
| VI/Aromatic | 96 | 0.00% | 100.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 47.80% | 34.40% | 0.00% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0517978444 | C -> T | LOC_Os05g30960.1 | missense_variant ; p.Arg99Trp; MODERATE | nonsynonymous_codon ; R99W | Average:77.105; most accessible tissue: Zhenshan97 young leaf, score: 89.226 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0517978444 | C -> DEL | LOC_Os05g30960.1 | N | frameshift_variant | Average:77.105; most accessible tissue: Zhenshan97 young leaf, score: 89.226 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0517978444 | NA | 1.03E-13 | mr1013 | 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 |
| vg0517978444 | NA | 4.24E-07 | mr1321 | 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 |
| vg0517978444 | NA | 3.59E-08 | mr1827 | 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 |
| vg0517978444 | NA | 9.92E-09 | mr1794_2 | 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 |