Search for Variation information by Variation ID:
Detailed information for vg0318816925:
| Variant ID: vg0318816925 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18816925 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 54. )
Flanking Sequence (100 bp) in Reference Genome:
GATGCGCATCCATTGCGGCAATAATACTGATAATCAAATTTGCAGGAAACCATCTGATATAGATCCGTCCGGGAAAGACTCTAACCCGACTAACGTGGAC[G/A]
CAAGTTCTTCCAAAGAAACCGGACCAACTGCTGAGGATCATCCAAGTGACAATCAGCCGGCAACCGATAATGTAGAACCCGGTGATCAACCCCTGACCGG
Reverse complement sequence
CCGGTCAGGGGTTGATCACCGGGTTCTACATTATCGGTTGCCGGCTGATTGTCACTTGGATGATCCTCAGCAGTTGGTCCGGTTTCTTTGGAAGAACTTG[C/T]
GTCCACGTTAGTCGGGTTAGAGTCTTTCCCGGACGGATCTATATCAGATGGTTTCCTGCAAATTTGATTATCAGTATTATTGCCGCAATGGATGCGCATC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.10% | 31.00% | 1.27% | 19.68% | NA |
| All Indica | 2759 | 23.40% | 49.30% | 1.12% | 26.21% | NA |
| All Japonica | 1512 | 97.00% | 1.40% | 1.46% | 0.13% | NA |
| Aus | 269 | 13.40% | 20.40% | 1.86% | 64.31% | NA |
| Indica I | 595 | 9.40% | 52.80% | 1.68% | 36.13% | NA |
| Indica II | 465 | 28.80% | 15.70% | 2.37% | 53.12% | NA |
| Indica III | 913 | 31.40% | 62.00% | 0.44% | 6.13% | NA |
| Indica Intermediate | 786 | 21.40% | 51.80% | 0.76% | 26.08% | NA |
| Temperate Japonica | 767 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 96.00% | 3.60% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 90.90% | 0.40% | 8.30% | 0.41% | NA |
| VI/Aromatic | 96 | 72.90% | 3.10% | 2.08% | 21.88% | NA |
| Intermediate | 90 | 61.10% | 26.70% | 0.00% | 12.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318816925 | G -> A | LOC_Os03g32900.1 | missense_variant ; p.Ala347Thr; MODERATE | nonsynonymous_codon ; A347T | Average:34.284; most accessible tissue: Minghui63 young leaf, score: 68.07 | benign  |
-0.28 |
TOLERATED | 1.00 |
| vg0318816925 | G -> DEL | LOC_Os03g32900.1 | N | frameshift_variant | Average:34.284; most accessible tissue: Minghui63 young leaf, score: 68.07 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0318816925 | NA | 9.21E-06 | mr1532 | 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 |
| vg0318816925 | NA | 4.01E-08 | mr1836 | 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 |
| vg0318816925 | 9.56E-07 | 9.55E-07 | mr1836 | 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 |
| vg0318816925 | NA | 4.78E-06 | mr1901 | 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 |
| vg0318816925 | NA | 7.30E-07 | mr1727_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 |