Search for Variation information by Variation ID:
Detailed information for vg0822310706:
| Variant ID: vg0822310706 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 22310706 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 59. )
Flanking Sequence (100 bp) in Reference Genome:
AACACCAGGAGACGGCGGATCCCTAGTCCAGCTGCCACTCTGAGTCCCGCAAGGAGTCCCTTGTACTCCGCCATATTGTTGGTCGCCCGAAAGTCGAGGC[A/G]
GACCAGGTATCTGAGGACGTCTCCGCTCGGCGAGGTCAACGTGACCCCCGCACCAGCGCCCTGAAGAGACAGGGAGCCGTCGAACTGCATCACCCAGTAG
Reverse complement sequence
CTACTGGGTGATGCAGTTCGACGGCTCCCTGTCTCTTCAGGGCGCTGGTGCGGGGGTCACGTTGACCTCGCCGAGCGGAGACGTCCTCAGATACCTGGTC[T/C]
GCCTCGACTTTCGGGCGACCAACAATATGGCGGAGTACAAGGGACTCCTTGCGGGACTCAGAGTGGCAGCTGGACTAGGGATCCGCCGTCTCCTGGTGTT
Allele Frequencies:
| 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 | 21.60% | 14.60% | 13.50% | 50.23% | NA |
| All Indica | 2759 | 1.90% | 1.30% | 19.54% | 77.27% | NA |
| All Japonica | 1512 | 60.70% | 35.00% | 2.98% | 1.32% | NA |
| Aus | 269 | 10.80% | 38.30% | 14.50% | 36.43% | NA |
| Indica I | 595 | 0.80% | 0.50% | 13.95% | 84.71% | NA |
| Indica II | 465 | 1.10% | 1.30% | 13.98% | 83.66% | NA |
| Indica III | 913 | 2.00% | 1.00% | 26.18% | 70.87% | NA |
| Indica Intermediate | 786 | 3.10% | 2.30% | 19.34% | 75.32% | NA |
| Temperate Japonica | 767 | 79.90% | 14.90% | 3.78% | 1.43% | NA |
| Tropical Japonica | 504 | 31.00% | 66.10% | 2.18% | 0.79% | NA |
| Japonica Intermediate | 241 | 61.80% | 34.00% | 2.07% | 2.07% | NA |
| VI/Aromatic | 96 | 3.10% | 7.30% | 3.12% | 86.46% | NA |
| Intermediate | 90 | 23.30% | 17.80% | 13.33% | 45.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0822310706 | A -> G | LOC_Os08g35390.1 | missense_variant ; p.Cys1404Arg; MODERATE | nonsynonymous_codon ; C1404R | Average:10.347; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
-0.747 |
TOLERATED | 1.00 |
| vg0822310706 | A -> DEL | LOC_Os08g35390.1 | N | frameshift_variant | Average:10.347; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0822310706 | NA | 2.21E-11 | Plant_height | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0822310706 | NA | 9.53E-06 | mr1063 | 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 |
| vg0822310706 | 9.24E-06 | 2.61E-07 | mr1177 | 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 |
| vg0822310706 | NA | 2.38E-06 | mr1479_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 |
| vg0822310706 | NA | 1.09E-08 | mr1794_2 | 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 |
| vg0822310706 | NA | 7.98E-09 | mr1851_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 |