Search for Variation information by Variation ID:
Detailed information for vg0708597974:
| Variant ID: vg0708597974 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 8597974 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 115. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTCATAGAGGTAGCCGAATTAATCATACTCTACGATCTCTGTTGGTCGTGAGTCGACGCCGGGGGAGCTGAAGTAGCCTTCCAATTGATCCGTCGAAA[T/C]
CGTGCCGAGTGGCTGGAGTATGACGCCGACTTCCCTGGAGCTAGGCCGGATCCATGCTAAAGCCGGATCCCGCTTAGGCCTACGGGGAGAAGACGTCCTT
Reverse complement sequence
AAGGACGTCTTCTCCCCGTAGGCCTAAGCGGGATCCGGCTTTAGCATGGATCCGGCCTAGCTCCAGGGAAGTCGGCGTCATACTCCAGCCACTCGGCACG[A/G]
TTTCGACGGATCAATTGGAAGGCTACTTCAGCTCCCCCGGCGTCGACTCACGACCAACAGAGATCGTAGAGTATGATTAATTCGGCTACCTCTATGACAA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.10% | 35.70% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 96.50% | 3.20% | 0.29% | 0.00% | NA |
| All Japonica | 1512 | 12.80% | 87.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 39.80% | 60.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.50% | 0.67% | 0.00% | NA |
| Indica II | 465 | 92.70% | 7.10% | 0.22% | 0.00% | NA |
| Indica III | 913 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.10% | 5.50% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 16.20% | 83.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 11.50% | 88.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.60% | 95.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 22.90% | 77.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 48.90% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0708597974 | T -> C | LOC_Os07g14990.1 | missense_variant ; p.Ile142Val; MODERATE | nonsynonymous_codon ; I142V | Average:41.299; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 | benign  |
-0.344 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0708597974 | 3.85E-06 | NA | mr1206 | 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 |
| vg0708597974 | NA | 2.82E-07 | mr1804 | 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 |
| vg0708597974 | NA | 3.07E-08 | mr1827 | 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 |
| vg0708597974 | NA | 2.71E-06 | mr1161_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 |