Search for Variation information by Variation ID:
Detailed information for vg0802219948:
| Variant ID: vg0802219948 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 2219948 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 363. )
Flanking Sequence (100 bp) in Reference Genome:
TTCTTTCCATCAAAGGTGGTTTTCACTGGCACGAAATGAGCTGATTTCGTGAGTCGATCCACGATTACCCAGATGGAGTCGTACCCGTTAGGGGTTCTTG[G/C]
CAAACCGGTGATGAAATCCATTCCGATCTCTTCCCATTTCCACTCGGGAATCGGTAGGGGTTGCAGCAGACCAGCTGGCCTCTGATGCTCTGCCTTGACT
Reverse complement sequence
AGTCAAGGCAGAGCATCAGAGGCCAGCTGGTCTGCTGCAACCCCTACCGATTCCCGAGTGGAAATGGGAAGAGATCGGAATGGATTTCATCACCGGTTTG[C/G]
CAAGAACCCCTAACGGGTACGACTCCATCTGGGTAATCGTGGATCGACTCACGAAATCAGCTCATTTCGTGCCAGTGAAAACCACCTTTGATGGAAAGAA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.00% | 5.50% | 28.29% | 4.23% | NA |
| All Indica | 2759 | 44.00% | 9.50% | 41.28% | 5.26% | NA |
| All Japonica | 1512 | 98.70% | 0.00% | 1.06% | 0.26% | NA |
| Aus | 269 | 25.70% | 0.00% | 57.99% | 16.36% | NA |
| Indica I | 595 | 32.40% | 6.60% | 50.08% | 10.92% | NA |
| Indica II | 465 | 57.20% | 8.40% | 27.31% | 7.10% | NA |
| Indica III | 913 | 46.00% | 12.60% | 40.53% | 0.88% | NA |
| Indica Intermediate | 786 | 42.60% | 8.70% | 43.77% | 4.96% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.91% | 0.26% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.79% | 0.20% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 2.07% | 0.41% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 6.25% | 1.04% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 22.22% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0802219948 | G -> C | LOC_Os08g04510.1 | missense_variant ; p.Pro1397Ala; MODERATE | nonsynonymous_codon ; P1397A | Average:9.219; most accessible tissue: Minghui63 young leaf, score: 20.156 | benign  |
1.084 |
DELETERIOUS | 0.01 |
| vg0802219948 | G -> DEL | LOC_Os08g04510.1 | N | frameshift_variant | Average:9.219; most accessible tissue: Minghui63 young leaf, score: 20.156 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0802219948 | 6.04E-06 | NA | mr1026 | 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 |
| vg0802219948 | 2.68E-06 | NA | mr1063 | 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 |
| vg0802219948 | 2.64E-06 | NA | mr1161 | 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 |
| vg0802219948 | 6.39E-08 | NA | mr1750 | 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 |