Search for Variation information by Variation ID:
Detailed information for vg1222490486:
| Variant ID: vg1222490486 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22490486 |
| Reference Allele: T | Alternative Allele: C,G |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 32. )
Flanking Sequence (100 bp) in Reference Genome:
TCATCGTTAGAGTCAAATATTCGTTTGCAGAACAATTGTCTGGAATCATCATCAGATAAGGGTTTCATTTCATAAACACCACCGCCTGCATGTTCTGCAA[T/C,G]
GACCTTGTTTCGCGTGGTTACAATTATTTTGCTACCAAGTTTAGCATCTTGCACAGCAAGTTTGATAGTATCCCACGCTGATTTTTTCCATACATCATCA
Reverse complement sequence
TGATGATGTATGGAAAAAATCAGCGTGGGATACTATCAAACTTGCTGTGCAAGATGCTAAACTTGGTAGCAAAATAATTGTAACCACGCGAAACAAGGTC[A/G,C]
TTGCAGAACATGCAGGCGGTGGTGTTTATGAAATGAAACCCTTATCTGATGATGATTCCAGACAATTGTTCTGCAAACGAATATTTGACTCTAACGATGA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.90% | 17.50% | 6.64% | 34.91% | G: 0.02% |
| All Indica | 2759 | 20.50% | 29.20% | 7.68% | 42.59% | NA |
| All Japonica | 1512 | 79.30% | 0.70% | 5.95% | 13.96% | G: 0.07% |
| Aus | 269 | 9.70% | 0.00% | 3.35% | 86.99% | NA |
| Indica I | 595 | 42.50% | 25.40% | 3.53% | 28.57% | NA |
| Indica II | 465 | 18.10% | 50.30% | 6.02% | 25.59% | NA |
| Indica III | 913 | 10.50% | 17.10% | 11.17% | 61.23% | NA |
| Indica Intermediate | 786 | 16.80% | 33.80% | 7.76% | 41.60% | NA |
| Temperate Japonica | 767 | 86.30% | 0.50% | 9.00% | 4.17% | NA |
| Tropical Japonica | 504 | 73.80% | 1.00% | 0.79% | 24.21% | G: 0.20% |
| Japonica Intermediate | 241 | 68.50% | 0.80% | 7.05% | 23.65% | NA |
| VI/Aromatic | 96 | 84.40% | 2.10% | 2.08% | 11.46% | NA |
| Intermediate | 90 | 67.80% | 10.00% | 1.11% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222490486 | T -> C | LOC_Os12g36720.1 | missense_variant ; p.Ile307Val; MODERATE | nonsynonymous_codon ; I307V | Average:17.434; most accessible tissue: Minghui63 panicle, score: 25.313 | benign  |
-0.877 |
TOLERATED | 1.00 |
| vg1222490486 | T -> DEL | LOC_Os12g36720.1 | N | frameshift_variant | Average:17.434; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg1222490486 | T -> G | LOC_Os12g36720.1 | missense_variant ; p.Ile307Leu; MODERATE | nonsynonymous_codon ; I307L | Average:17.434; most accessible tissue: Minghui63 panicle, score: 25.313 | benign |
0.023 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1222490486 | NA | 2.62E-09 | mr1011 | 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 |
| vg1222490486 | NA | 1.45E-06 | mr1011 | 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 |
| vg1222490486 | 7.79E-06 | 7.76E-06 | mr1012 | 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 |
| vg1222490486 | NA | 4.63E-13 | mr1031 | 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 |
| vg1222490486 | NA | 4.84E-06 | mr1031 | 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 |
| vg1222490486 | NA | 3.29E-12 | mr1034 | 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 |
| vg1222490486 | NA | 3.62E-13 | mr1056 | 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 |
| vg1222490486 | NA | 9.60E-06 | mr1056 | 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 |
| vg1222490486 | NA | 2.81E-06 | mr1279 | 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 |
| vg1222490486 | NA | 9.22E-07 | mr1038_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 |