Search for Variation information by Variation ID:
Detailed information for vg0905283103:
| Variant ID: vg0905283103 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5283103 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.59, T: 0.41, others allele: 0.00, population size: 49. )
Flanking Sequence (100 bp) in Reference Genome:
AGCCTTTGACGCCATCAAGGCCCCGGGGATGGTGCTCCAGCCGTCCCAGCCGATTATCGGTGTAACGCCGGGGCACACTTGGCCGTTAGGTCATATCGAC[T/C]
TCCCGGTCACCTTCGGTGGATCCGCCAACTTCCGCACGGAGCGGGTGAACTTCGATGTGGCGGACCTCAGTCTGCCCTACAACGCGGTCCTAGGGAGGCC
Reverse complement sequence
GGCCTCCCTAGGACCGCGTTGTAGGGCAGACTGAGGTCCGCCACATCGAAGTTCACCCGCTCCGTGCGGAAGTTGGCGGATCCACCGAAGGTGACCGGGA[A/G]
GTCGATATGACCTAACGGCCAAGTGTGCCCCGGCGTTACACCGATAATCGGCTGGGACGGCTGGAGCACCATCCCCGGGGCCTTGATGGCGTCAAAGGCT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.60% | 1.00% | 16.95% | 50.42% | NA |
| All Indica | 2759 | 6.20% | 1.60% | 22.07% | 70.21% | NA |
| All Japonica | 1512 | 80.20% | 0.10% | 1.26% | 18.39% | NA |
| Aus | 269 | 23.40% | 0.70% | 58.74% | 17.10% | NA |
| Indica I | 595 | 9.40% | 0.50% | 6.05% | 84.03% | NA |
| Indica II | 465 | 7.70% | 2.40% | 38.71% | 51.18% | NA |
| Indica III | 913 | 3.00% | 2.50% | 21.58% | 72.95% | NA |
| Indica Intermediate | 786 | 6.50% | 0.80% | 24.94% | 67.81% | NA |
| Temperate Japonica | 767 | 89.70% | 0.10% | 0.26% | 9.91% | NA |
| Tropical Japonica | 504 | 81.90% | 0.20% | 0.60% | 17.26% | NA |
| Japonica Intermediate | 241 | 46.50% | 0.00% | 5.81% | 47.72% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 7.29% | 87.50% | NA |
| Intermediate | 90 | 47.80% | 1.10% | 8.89% | 42.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0905283103 | T -> DEL | LOC_Os09g09760.1 | N | frameshift_variant | Average:14.054; most accessible tissue: Minghui63 root, score: 36.81 | N | N | N | N |
| vg0905283103 | T -> C | LOC_Os09g09760.1 | missense_variant ; p.Phe562Leu; MODERATE | nonsynonymous_codon ; F562L | Average:14.054; most accessible tissue: Minghui63 root, score: 36.81 | probably damaging  |
-2.343 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0905283103 | NA | 1.46E-09 | mr1945 | 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 |
| vg0905283103 | 1.88E-06 | NA | mr1539_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 |