Search for Variation information by Variation ID:
Detailed information for vg0627307052:
| Variant ID: vg0627307052 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 27307052 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )
Flanking Sequence (100 bp) in Reference Genome:
GTGACCTAATGCAAGGACATGCATGTCCATTACTGGACCTGGATGCCACTCTTGTAGACGGAGCCGGCCTTAAAGGTTTCGGGGATTACATCGTCGACGA[T/C]
GCGATAGCCACCGTTCTTGACAAGGAAGCGGACGGATAAGGGGCCCTTGAGCGGTGCATCACTTTTGATTTTCCAGGTGTTAGCCGATGACTCCTTGAGC
Reverse complement sequence
GCTCAAGGAGTCATCGGCTAACACCTGGAAAATCAAAAGTGATGCACCGCTCAAGGGCCCCTTATCCGTCCGCTTCCTTGTCAAGAACGGTGGCTATCGC[A/G]
TCGTCGACGATGTAATCCCCGAAACCTTTAAGGCCGGCTCCGTCTACAAGAGTGGCATCCAGGTCCAGTAATGGACATGCATGTCCTTGCATTAGGTCAC
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 | 92.70% | 3.70% | 3.58% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 78.30% | 11.00% | 10.65% | 0.00% | NA |
| Aus | 269 | 98.50% | 0.00% | 1.49% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 67.80% | 16.40% | 15.78% | 0.00% | NA |
| Tropical Japonica | 504 | 90.50% | 6.20% | 3.37% | 0.00% | NA |
| Japonica Intermediate | 241 | 86.30% | 4.10% | 9.54% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0627307052 | T -> C | LOC_Os06g45160.1 | missense_variant ; p.Ile96Val; MODERATE | nonsynonymous_codon ; I96V | Average:66.368; most accessible tissue: Zhenshan97 young leaf, score: 76.44 | benign  |
-1.41 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0627307052 | 2.64E-06 | 2.64E-06 | mr1910 | 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 |