Search for Variation information by Variation ID:
Detailed information for vg0303700417:
| Variant ID: vg0303700417 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 3700417 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.02, others allele: 0.00, population size: 309. )
Flanking Sequence (100 bp) in Reference Genome:
AAAGTAGTGTTCTCCAAATGACAGAATTAGGCTCACATTTCATCGTATCAATGAACTCAAATGCTTCTTTTAGTAGCCCAGCACGACCCAGCATGTCCAC[C/A]
ATGCAACCGTAGTGCTTGATATTGGGTTCAACCCTGTACTTATGCTGCATCAAGTTGAAGAATTCACGTCCCTTGTCAACCATCCCGCCGTGGCTGCAGG
Reverse complement sequence
CCTGCAGCCACGGCGGGATGGTTGACAAGGGACGTGAATTCTTCAACTTGATGCAGCATAAGTACAGGGTTGAACCCAATATCAAGCACTACGGTTGCAT[G/T]
GTGGACATGCTGGGTCGTGCTGGGCTACTAAAAGAAGCATTTGAGTTCATTGATACGATGAAATGTGAGCCTAATTCTGTCATTTGGAGAACACTACTTT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.20% | 47.60% | 0.06% | 0.15% | NA |
| All Indica | 2759 | 22.00% | 77.70% | 0.07% | 0.22% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 72.90% | 27.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 14.80% | 85.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 13.10% | 86.70% | 0.00% | 0.22% | NA |
| Indica III | 913 | 30.80% | 68.80% | 0.22% | 0.22% | NA |
| Indica Intermediate | 786 | 22.40% | 77.40% | 0.00% | 0.25% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 31.10% | 1.11% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0303700417 | C -> A | LOC_Os03g07234.1 | missense_variant ; p.Met390Ile; MODERATE | nonsynonymous_codon ; M390I | Average:60.27; most accessible tissue: Zhenshan97 young leaf, score: 82.982 | benign  |
0.161 |
TOLERATED | 0.10 |
| vg0303700417 | C -> DEL | LOC_Os03g07234.1 | N | frameshift_variant | Average:60.27; most accessible tissue: Zhenshan97 young leaf, score: 82.982 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0303700417 | NA | 1.27E-07 | mr1781 | 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 |
| vg0303700417 | NA | 3.60E-06 | mr1990 | 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 |
| vg0303700417 | NA | 5.92E-07 | mr1045_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 |
| vg0303700417 | NA | 9.87E-06 | mr1053_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 |
| vg0303700417 | NA | 3.57E-23 | mr1316_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 |
| vg0303700417 | NA | 2.35E-06 | mr1925_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 |