Search for Variation information by Variation ID:
Detailed information for vg0402981114:
| Variant ID: vg0402981114 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2981114 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 61. )
Flanking Sequence (100 bp) in Reference Genome:
GATAATTTATGCTACCTTGCAGAGATCTTATTTATGGAAAAATATAAGGAAGATACGCCTTTCGCATAACATGAGGGCTCTATATGACCCGTGGTTTTCG[G/A]
ATTATCTACTTCGGATTGGAAACGGGACGGAAAACACAATCGGAGATGATTACGTCTGTCTGCCTGATGAAATTGTCATTGGTTATGTAGACATTGAAGA
Reverse complement sequence
TCTTCAATGTCTACATAACCAATGACAATTTCATCAGGCAGACAGACGTAATCATCTCCGATTGTGTTTTCCGTCCCGTTTCCAATCCGAAGTAGATAAT[C/T]
CGAAAACCACGGGTCATATAGAGCCCTCATGTTATGCGAAAGGCGTATCTTCCTTATATTTTTCCATAAATAAGATCTCTGCAAGGTAGCATAAATTATC
Allele Frequencies:
| 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 | 44.40% | 24.60% | 7.87% | 23.17% | NA |
| All Indica | 2759 | 39.40% | 35.70% | 9.46% | 15.44% | NA |
| All Japonica | 1512 | 50.90% | 5.20% | 3.90% | 39.95% | NA |
| Aus | 269 | 52.40% | 27.90% | 15.61% | 4.09% | NA |
| Indica I | 595 | 25.50% | 29.40% | 9.75% | 35.29% | NA |
| Indica II | 465 | 32.50% | 46.00% | 12.47% | 9.03% | NA |
| Indica III | 913 | 51.00% | 35.60% | 6.57% | 6.79% | NA |
| Indica Intermediate | 786 | 40.60% | 34.40% | 10.81% | 14.25% | NA |
| Temperate Japonica | 767 | 76.40% | 7.70% | 4.04% | 11.86% | NA |
| Tropical Japonica | 504 | 17.30% | 1.40% | 3.97% | 77.38% | NA |
| Japonica Intermediate | 241 | 40.20% | 5.40% | 3.32% | 51.04% | NA |
| VI/Aromatic | 96 | 51.00% | 10.40% | 1.04% | 37.50% | NA |
| Intermediate | 90 | 55.60% | 14.40% | 10.00% | 20.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402981114 | G -> DEL | LOC_Os04g05800.1 | N | frameshift_variant | Average:11.061; most accessible tissue: Zhenshan97 young leaf, score: 23.991 | N | N | N | N |
| vg0402981114 | G -> A | LOC_Os04g05800.1 | missense_variant ; p.Asp870Asn; MODERATE | nonsynonymous_codon ; D870N | Average:11.061; most accessible tissue: Zhenshan97 young leaf, score: 23.991 | benign  |
1.495 |
TOLERATED | 0.07 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402981114 | 1.00E-06 | 1.55E-06 | mr1968_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 |