Search for Variation information by Variation ID:
Detailed information for vg0100096616:
| Variant ID: vg0100096616 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 96616 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.52, C: 0.48, others allele: 0.00, population size: 100. )
Flanking Sequence (100 bp) in Reference Genome:
CCGCTCGTGGACCATCAGGTGGCGGCGTCGCTGAAGGAGAAAATCGCCAAGGAGGCGTCTGACACTGCTGCCGCTGCTGCCACAACGAGTGGCGGCAACG[C/T]
TCCGAAAAAGGGGAGGAAATTCTCCTCTGTGATCGGACATCGTCGAAAGACACCCACCCTCTCGGTAAGTTCTCCTTGTCCTTCATCGCGTAGTCGGGAA
Reverse complement sequence
TTCCCGACTACGCGATGAAGGACAAGGAGAACTTACCGAGAGGGTGGGTGTCTTTCGACGATGTCCGATCACAGAGGAGAATTTCCTCCCCTTTTTCGGA[G/A]
CGTTGCCGCCACTCGTTGTGGCAGCAGCGGCAGCAGTGTCAGACGCCTCCTTGGCGATTTTCTCCTTCAGCGACGCCGCCACCTGATGGTCCACGAGCGG
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 | 73.30% | 24.90% | 0.78% | 1.06% | NA |
| All Indica | 2759 | 66.30% | 31.20% | 0.76% | 1.70% | NA |
| All Japonica | 1512 | 96.50% | 2.40% | 0.99% | 0.13% | NA |
| Aus | 269 | 8.90% | 91.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 28.10% | 71.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 94.40% | 3.70% | 1.51% | 0.43% | NA |
| Indica III | 913 | 80.60% | 14.10% | 1.42% | 3.83% | NA |
| Indica Intermediate | 786 | 62.00% | 36.60% | 0.13% | 1.27% | NA |
| Temperate Japonica | 767 | 98.60% | 0.50% | 0.78% | 0.13% | NA |
| Tropical Japonica | 504 | 93.70% | 6.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.40% | 3.32% | 0.41% | NA |
| VI/Aromatic | 96 | 80.20% | 18.80% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 81.10% | 17.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0100096616 | C -> T | LOC_Os01g01200.1 | missense_variant ; p.Ala287Val; MODERATE | nonsynonymous_codon ; A287I | Average:59.815; most accessible tissue: Minghui63 young leaf, score: 82.907 | benign  |
0.982 |
TOLERATED | 0.12 |
| vg0100096616 | C -> T | LOC_Os01g01200.1 | missense_variant ; p.Ala287Val; MODERATE | nonsynonymous_codon ; A287V | Average:59.815; most accessible tissue: Minghui63 young leaf, score: 82.907 | benign |
-0.134 |
TOLERATED | 1.00 |
| vg0100096616 | C -> DEL | LOC_Os01g01200.1 | N | frameshift_variant | Average:59.815; most accessible tissue: Minghui63 young leaf, score: 82.907 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100096616 | NA | 8.09E-06 | mr1531 | Ind_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 |
| vg0100096616 | NA | 2.08E-10 | mr1662 | 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 |
| vg0100096616 | 2.81E-06 | NA | mr1718 | 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 |
| vg0100096616 | NA | 4.74E-07 | mr1531_2 | Ind_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 |