Search for Variation information by Variation ID:
Detailed information for vg1000477580:
| Variant ID: vg1000477580 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 477580 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 88. )
Flanking Sequence (100 bp) in Reference Genome:
TAGAAATTTCAATATGCCAAGTTGTCCGATAATAGCTAACCCCTACGTGAGGATCCCTCTCCTCTCTCAAACCGCGTTTTAGTAACCCTGTATTGCTCTG[G/A]
TAGTTCAAGCTGCACAACACGGCTAGGTGGAGTTAGCACCCTTCTGGTGTCTATCCATTCTCTGTATTGACATCTCCTTGGTGGTTCCTGGGAGAAAAGA
Reverse complement sequence
TCTTTTCTCCCAGGAACCACCAAGGAGATGTCAATACAGAGAATGGATAGACACCAGAAGGGTGCTAACTCCACCTAGCCGTGTTGTGCAGCTTGAACTA[C/T]
CAGAGCAATACAGGGTTACTAAAACGCGGTTTGAGAGAGGAGAGGGATCCTCACGTAGGGGTTAGCTATTATCGGACAACTTGGCATATTGAAATTTCTA
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 | 76.10% | 16.30% | 0.36% | 7.19% | NA |
| All Indica | 2759 | 69.30% | 26.90% | 0.18% | 3.59% | NA |
| All Japonica | 1512 | 98.40% | 1.10% | 0.07% | 0.46% | NA |
| Aus | 269 | 28.30% | 0.00% | 3.72% | 68.03% | NA |
| Indica I | 595 | 80.30% | 19.50% | 0.17% | 0.00% | NA |
| Indica II | 465 | 53.30% | 45.80% | 0.00% | 0.86% | NA |
| Indica III | 913 | 73.90% | 20.40% | 0.22% | 5.48% | NA |
| Indica Intermediate | 786 | 65.10% | 28.90% | 0.25% | 5.73% | NA |
| Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.20% | 1.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.40% | 1.70% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 53.10% | 3.10% | 1.04% | 42.71% | NA |
| Intermediate | 90 | 76.70% | 12.20% | 0.00% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000477580 | G -> A | LOC_Os10g01740.1 | missense_variant ; p.Pro31Ser; MODERATE | nonsynonymous_codon ; P31S | Average:18.201; most accessible tissue: Minghui63 panicle, score: 25.313 | possibly damaging  |
1.831 |
TOLERATED | 0.12 |
| vg1000477580 | G -> DEL | LOC_Os10g01740.1 | N | frameshift_variant | Average:18.201; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000477580 | NA | 3.00E-08 | mr1709 | 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 |
| vg1000477580 | NA | 8.57E-09 | mr1709_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 |
| vg1000477580 | NA | 5.08E-08 | mr1709_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 |