Search for Variation information by Variation ID:
Detailed information for vg0718976518:
| Variant ID: vg0718976518 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 18976518 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 57. )
Flanking Sequence (100 bp) in Reference Genome:
CGCTGTTTTGGTTCGTGCTCTTCATGTCTTGGGCTCTCGTGTAGAATGTGTACCCATTGATCTCATATCCCTGAAATGTCGCAATCGACCCAGACGGTCC[A/C]
CTCGCCAGGAAGGCAAGTTGTTGGTTGATCGACTCGTTACCCATGAGATGTTGTCGTAGCCACGCGGGGAAAGTATCAATGTGATGCCGTGTAATCCATG
Reverse complement sequence
CATGGATTACACGGCATCACATTGATACTTTCCCCGCGTGGCTACGACAACATCTCATGGGTAACGAGTCGATCAACCAACAACTTGCCTTCCTGGCGAG[T/G]
GGACCGTCTGGGTCGATTGCGACATTTCAGGGATATGAGATCAATGGGTACACATTCTACACGAGAGCCCAAGACATGAAGAGCACGAACCAAAACAGCG
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 | 11.10% | 10.30% | 27.47% | 51.18% | NA |
| All Indica | 2759 | 0.60% | 1.10% | 34.32% | 63.94% | NA |
| All Japonica | 1512 | 31.90% | 29.20% | 13.03% | 25.86% | NA |
| Aus | 269 | 0.00% | 1.10% | 28.62% | 70.26% | NA |
| Indica I | 595 | 0.50% | 0.70% | 23.53% | 75.29% | NA |
| Indica II | 465 | 0.00% | 2.20% | 28.60% | 69.25% | NA |
| Indica III | 913 | 0.30% | 0.70% | 44.91% | 54.11% | NA |
| Indica Intermediate | 786 | 1.40% | 1.40% | 33.59% | 63.61% | NA |
| Temperate Japonica | 767 | 35.30% | 50.20% | 11.47% | 3.00% | NA |
| Tropical Japonica | 504 | 23.80% | 4.60% | 15.67% | 55.95% | NA |
| Japonica Intermediate | 241 | 37.80% | 14.10% | 12.45% | 35.68% | NA |
| VI/Aromatic | 96 | 17.70% | 0.00% | 36.46% | 45.83% | NA |
| Intermediate | 90 | 7.80% | 11.10% | 46.67% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0718976518 | A -> DEL | LOC_Os07g31910.1 | N | frameshift_variant | Average:18.129; most accessible tissue: Minghui63 young leaf, score: 27.355 | N | N | N | N |
| vg0718976518 | A -> C | LOC_Os07g31910.1 | missense_variant ; p.Ser231Arg; MODERATE | nonsynonymous_codon ; S231R | Average:18.129; most accessible tissue: Minghui63 young leaf, score: 27.355 | possibly damaging  |
-1.753 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0718976518 | 1.11E-06 | NA | mr1404_2 | 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 |