| Variant ID: vg0500016244 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 16244 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCATCCGTGCCACGGGAGCGAAGGCATCGTCGTAGTCGATCCCCTCCTGCTGCACGAAACCGCGTGCCACCAAGCGAGCCTTGTGCTTGACGATGGCTCT[A/G]
GCTTCATCCCTCTTCAGCTTGAACACCCACTTAAGGGTGATCCCGCGGTGACCACGAGGGAGGTCAGCAAGCTCCCAGGTGCGGTTCTCCTGAACCGCGT
ACGCGGTTCAGGAGAACCGCACCTGGGAGCTTGCTGACCTCCCTCGTGGTCACCGCGGGATCACCCTTAAGTGGGTGTTCAAGCTGAAGAGGGATGAAGC[T/C]
AGAGCCATCGTCAAGCACAAGGCTCGCTTGGTGGCACGCGGTTTCGTGCAGCAGGAGGGGATCGACTACGACGATGCCTTCGCTCCCGTGGCACGGATGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.00% | 0.80% | 20.91% | 41.37% | NA |
| All Indica | 2759 | 4.90% | 1.20% | 33.38% | 60.53% | NA |
| All Japonica | 1512 | 96.40% | 0.00% | 0.20% | 3.37% | NA |
| Aus | 269 | 4.50% | 0.40% | 19.70% | 75.46% | NA |
| Indica I | 595 | 2.50% | 0.80% | 13.28% | 83.36% | NA |
| Indica II | 465 | 6.00% | 2.20% | 20.43% | 71.40% | NA |
| Indica III | 913 | 3.70% | 0.10% | 56.08% | 40.09% | NA |
| Indica Intermediate | 786 | 7.50% | 2.00% | 29.90% | 60.56% | NA |
| Temperate Japonica | 767 | 94.50% | 0.00% | 0.26% | 5.22% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.00% | 0.00% | 4.56% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 0.00% | 9.38% | NA |
| Intermediate | 90 | 60.00% | 3.30% | 12.22% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0500016244 | A -> DEL | LOC_Os05g00996.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0500016244 | A -> G | LOC_Os05g00996.1 | synonymous_variant ; p.Ala551Ala; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0500016244 | NA | 5.09E-06 | mr1334 | 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 |
| vg0500016244 | NA | 1.47E-06 | mr1527 | 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 |
| vg0500016244 | NA | 6.27E-06 | 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 |
| vg0500016244 | NA | 6.38E-06 | 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 |
| vg0500016244 | NA | 2.17E-24 | mr1588_2 | 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 |
| vg0500016244 | 4.94E-06 | NA | mr1718_2 | 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 |