| Variant ID: vg0319498343 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19498343 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAGCAGTTCAAATTCTCGGCCAAGCACTTTTCCTGATAGCCTTTGGCTCGGGGGAGAACAGACGCGAAGAGCAAATACTGTTCGACGTCGTCGACATCCC[A/G]
TACAACTACAACGCCATCTTCGGCCGTGCAACCCTGAACAAGTTCGAAGCCATTTCCCACCACAATTATCTCAAGCTCAAGATGCCCGGCCCGACAGGGG
CCCCTGTCGGGCCGGGCATCTTGAGCTTGAGATAATTGTGGTGGGAAATGGCTTCGAACTTGTTCAGGGTTGCACGGCCGAAGATGGCGTTGTAGTTGTA[T/C]
GGGATGTCGACGACGTCGAACAGTATTTGCTCTTCGCGTCTGTTCTCCCCCGAGCCAAAGGCTATCAGGAAAAGTGCTTGGCCGAGAATTTGAACTGCTT
| 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 | 61.60% | 27.20% | 5.21% | 6.03% | NA |
| All Indica | 2759 | 86.50% | 2.60% | 5.29% | 5.58% | NA |
| All Japonica | 1512 | 14.20% | 73.30% | 5.03% | 7.54% | NA |
| Aus | 269 | 89.60% | 8.90% | 1.12% | 0.37% | NA |
| Indica I | 595 | 92.10% | 1.20% | 4.37% | 2.35% | NA |
| Indica II | 465 | 89.20% | 3.20% | 3.87% | 3.66% | NA |
| Indica III | 913 | 83.20% | 1.80% | 6.35% | 8.65% | NA |
| Indica Intermediate | 786 | 84.40% | 4.50% | 5.60% | 5.60% | NA |
| Temperate Japonica | 767 | 0.30% | 90.70% | 4.30% | 4.69% | NA |
| Tropical Japonica | 504 | 34.50% | 47.60% | 5.36% | 12.50% | NA |
| Japonica Intermediate | 241 | 15.80% | 71.40% | 6.64% | 6.22% | NA |
| VI/Aromatic | 96 | 26.00% | 47.90% | 12.50% | 13.54% | NA |
| Intermediate | 90 | 47.80% | 38.90% | 10.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319498343 | A -> DEL | LOC_Os03g34240.1 | N | frameshift_variant | Average:34.218; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 | N | N | N | N |
| vg0319498343 | A -> G | LOC_Os03g34240.1 | synonymous_variant ; p.Pro800Pro; LOW | synonymous_codon | Average:34.218; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0319498343 | NA | 5.76E-08 | mr1136 | 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 |
| vg0319498343 | NA | 5.81E-07 | mr1718 | 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 |
| vg0319498343 | 7.43E-06 | 3.32E-11 | mr1750 | 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 |
| vg0319498343 | 9.24E-07 | 9.23E-07 | mr1987 | 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 |
| vg0319498343 | NA | 2.34E-10 | mr1718_2 | 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 |