Search for Variation information by Variation ID:
Detailed information for vg0314712121:
| Variant ID: vg0314712121 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 14712121 |
| Reference Allele: C | Alternative Allele: G,A |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, G: 0.30, others allele: 0.00, population size: 76. )
Flanking Sequence (100 bp) in Reference Genome:
TTGGCATCCATCAAGGGAGAAACATACAAGTATCTTATGAGTTCTACCATCCCATGAGCTCGGCTAGGCAGTTTGGGATGGGACAGCTGCCAATCGGCTT[C/G,A]
TATTTTGCCGATAAAATTCAATGCAGAGGCAAAATCTCATCAACATTGATGATGGATCGACTGCTCAACATCCCAGGACCCCCTTTGGGCAGCATCGATA
Reverse complement sequence
TATCGATGCTGCCCAAAGGGGGTCCTGGGATGTTGAGCAGTCGATCCATCATCAATGTTGATGAGATTTTGCCTCTGCATTGAATTTTATCGGCAAAATA[G/C,T]
AAGCCGATTGGCAGCTGTCCCATCCCAAACTGCCTAGCCGAGCTCATGGGATGGTAGAACTCATAAGATACTTGTATGTTTCTCCCTTGATGGATGCCAA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.60% | 24.40% | 19.57% | 5.88% | A: 0.63% |
| All Indica | 2759 | 25.60% | 40.60% | 29.21% | 3.48% | A: 1.09% |
| All Japonica | 1512 | 98.80% | 0.10% | 0.40% | 0.66% | NA |
| Aus | 269 | 2.60% | 1.50% | 34.94% | 60.97% | NA |
| Indica I | 595 | 21.00% | 42.40% | 34.62% | 2.02% | NA |
| Indica II | 465 | 10.80% | 21.30% | 63.44% | 3.87% | A: 0.65% |
| Indica III | 913 | 35.90% | 51.90% | 7.89% | 2.52% | A: 1.75% |
| Indica Intermediate | 786 | 25.80% | 37.70% | 29.64% | 5.47% | A: 1.40% |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 0.20% | 0.20% | 1.98% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.40% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 88.50% | 5.20% | 2.08% | 4.17% | NA |
| Intermediate | 90 | 55.60% | 21.10% | 18.89% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0314712121 | C -> A | LOC_Os03g25700.1 | missense_variant ; p.Phe419Leu; MODERATE | nonsynonymous_codon ; F419L | Average:57.278; most accessible tissue: Zhenshan97 panicle, score: 74.671 | benign  |
-0.899 |
TOLERATED | 1.00 |
| vg0314712121 | C -> DEL | LOC_Os03g25700.1 | N | frameshift_variant | Average:57.278; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
| vg0314712121 | C -> G | LOC_Os03g25700.1 | missense_variant ; p.Phe419Leu; MODERATE | nonsynonymous_codon ; F419L | Average:57.278; most accessible tissue: Zhenshan97 panicle, score: 74.671 | benign |
-0.899 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0314712121 | NA | 3.30E-06 | mr1507 | 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 |
| vg0314712121 | NA | 4.44E-14 | mr1542 | 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 |
| vg0314712121 | 1.84E-06 | 6.27E-09 | mr1604 | 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 |
| vg0314712121 | NA | 5.82E-06 | mr1811 | 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 |
| vg0314712121 | 2.50E-06 | 1.27E-08 | mr1886 | 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 |
| vg0314712121 | NA | 5.31E-06 | mr1898 | 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 |
| vg0314712121 | NA | 1.09E-12 | mr1542_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 |