Search for Variation information by Variation ID:
Detailed information for vg0714933670:
| Variant ID: vg0714933670 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14933670 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACCGAAGCGAACCTGATTTCCAGGTTTAGCCCTTTGCACATCTCATTGAACTTGTCAGAGTCGAATTGCTTGCCGTTGTCGGTGATGAATTCTTTTGGTA[T/C]
TCCGAAATGGCAAACAATGTTTTTCCTCACAAACTTCTGTACAGCTGCCGAAGTGATCACGCCGAGTGGTTCGGCCTCGATCCATCGGGAGAAGTATTCG
Reverse complement sequence
CGAATACTTCTCCCGATGGATCGAGGCCGAACCACTCGGCGTGATCACTTCGGCAGCTGTACAGAAGTTTGTGAGGAAAAACATTGTTTGCCATTTCGGA[A/G]
TACCAAAAGAATTCATCACCGACAACGGCAAGCAATTCGACTCTGACAAGTTCAATGAGATGTGCAAAGGGCTAAACCTGGAAATCAGGTTCGCTTCGGT
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 | 59.00% | 37.40% | 1.10% | 2.50% | NA |
| All Indica | 2759 | 85.10% | 9.50% | 1.81% | 3.52% | NA |
| All Japonica | 1512 | 6.70% | 93.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 90.00% | 2.20% | 0.37% | 7.43% | NA |
| Indica I | 595 | 68.20% | 24.40% | 1.01% | 6.39% | NA |
| Indica II | 465 | 90.50% | 5.60% | 0.43% | 3.44% | NA |
| Indica III | 913 | 95.50% | 1.00% | 2.63% | 0.88% | NA |
| Indica Intermediate | 786 | 82.70% | 10.60% | 2.29% | 4.45% | NA |
| Temperate Japonica | 767 | 12.10% | 87.70% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 0.60% | 99.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 55.20% | 44.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 47.80% | 51.10% | 0.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714933670 | T -> DEL | LOC_Os07g26030.1 | N | frameshift_variant | Average:21.751; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0714933670 | T -> C | LOC_Os07g26030.1 | missense_variant ; p.Ile574Val; MODERATE | nonsynonymous_codon ; I574V | Average:21.751; most accessible tissue: Zhenshan97 panicle, score: 36.038 | benign  |
-0.751 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714933670 | NA | 3.92E-10 | mr1195 | 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 |
| vg0714933670 | 3.93E-06 | NA | mr1218 | Ind_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 |
| vg0714933670 | NA | 3.01E-13 | mr1281 | 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 |
| vg0714933670 | NA | 3.34E-09 | mr1722 | 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 |
| vg0714933670 | NA | 1.03E-17 | mr1281_2 | 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 |
| vg0714933670 | NA | 3.49E-06 | mr1982_2 | 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 |