Search for Variation information by Variation ID:
Detailed information for vg0711810587:
| Variant ID: vg0711810587 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 11810587 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.67, G: 0.33, others allele: 0.00, population size: 39. )
Flanking Sequence (100 bp) in Reference Genome:
CACCACCAATTCCGAATCACCAAAAGCCTCCACGTGTTTAGCTCCAACCATCTCCATAACTTGTAAGCCGAACAATAAAGCATTGTATTCGGCTTGATTA[T/G]
TTGTACAATAATACTCCAAACGAACCGATGCTTCATAACACATGCCATTAGGTGAAAACAAAACTATCAATATGCCTTGACCTTCTTTGCAAGAAGAACC
Reverse complement sequence
GGTTCTTCTTGCAAAGAAGGTCAAGGCATATTGATAGTTTTGTTTTCACCTAATGGCATGTGTTATGAAGCATCGGTTCGTTTGGAGTATTATTGTACAA[A/C]
TAATCAAGCCGAATACAATGCTTTATTGTTCGGCTTACAAGTTATGGAGATGGTTGGAGCTAAACACGTGGAGGCTTTTGGTGATTCGGAATTGGTGGTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.50% | 32.20% | 0.59% | 7.68% | NA |
| All Indica | 2759 | 92.60% | 5.80% | 0.29% | 1.30% | NA |
| All Japonica | 1512 | 1.90% | 80.20% | 0.79% | 17.13% | NA |
| Aus | 269 | 62.80% | 32.70% | 1.12% | 3.35% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 92.30% | 7.10% | 0.65% | 0.00% | NA |
| Indica III | 913 | 93.80% | 6.00% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 86.00% | 9.00% | 0.51% | 4.45% | NA |
| Temperate Japonica | 767 | 2.00% | 67.30% | 1.56% | 29.20% | NA |
| Tropical Japonica | 504 | 0.80% | 98.80% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 4.10% | 82.20% | 0.00% | 13.69% | NA |
| VI/Aromatic | 96 | 18.80% | 17.70% | 4.17% | 59.38% | NA |
| Intermediate | 90 | 45.60% | 51.10% | 1.11% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0711810587 | T -> DEL | LOC_Os07g20450.1 | N | frameshift_variant | Average:34.912; most accessible tissue: Zhenshan97 flag leaf, score: 50.663 | N | N | N | N |
| vg0711810587 | T -> G | LOC_Os07g20450.1 | missense_variant ; p.Asn142Thr; MODERATE | nonsynonymous_codon | Average:34.912; most accessible tissue: Zhenshan97 flag leaf, score: 50.663 | possibly damaging  |
1.672 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0711810587 | NA | 8.31E-06 | mr1329_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 |
| vg0711810587 | NA | 4.57E-10 | mr1851_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 |
| vg0711810587 | 3.30E-06 | NA | mr1918_2 | 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 |
| vg0711810587 | 4.72E-06 | NA | mr1929_2 | 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 |