Search for Variation information by Variation ID:
Detailed information for vg0712504949:
| Variant ID: vg0712504949 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 12504949 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 309. )
Flanking Sequence (100 bp) in Reference Genome:
CGTGCAAAAGATGCACTTTTCAAGGTTAGCAAACAAACGTGCATCGCGTAGAGCATTAAAAACAGCATGTAAATGATCCATGTGTTCATCCAAAGACTTG[C/T]
TGTAAATCAATATGTCATCAAAGTAAACTACCACAAATCGTCCAATAAAAGGCCTTAAAACCTCATTCATTAAGCGCATGAAAGTACTAGGTGCATTAGT
Reverse complement sequence
ACTAATGCACCTAGTACTTTCATGCGCTTAATGAATGAGGTTTTAAGGCCTTTTATTGGACGATTTGTGGTAGTTTACTTTGATGACATATTGATTTACA[G/A]
CAAGTCTTTGGATGAACACATGGATCATTTACATGCTGTTTTTAATGCTCTACGCGATGCACGTTTGTTTGCTAACCTTGAAAAGTGCATCTTTTGCACG
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 | 96.30% | 0.30% | 2.41% | 1.06% | NA |
| All Indica | 2759 | 99.40% | 0.40% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 89.60% | 0.00% | 7.14% | 3.31% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.20% | 0.50% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.70% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.40% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 82.40% | 0.00% | 13.04% | 4.56% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 91.30% | 0.00% | 2.90% | 5.81% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0712504949 | C -> DEL | LOC_Os07g22310.1 | N | frameshift_variant | Average:26.07; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0712504949 | C -> T | LOC_Os07g22310.1 | missense_variant ; p.Ser1120Asn; MODERATE | nonsynonymous_codon ; S1120N | Average:26.07; most accessible tissue: Zhenshan97 panicle, score: 39.652 | benign  |
0.688 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0712504949 | 3.30E-06 | 6.88E-07 | mr1042 | 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 |
| vg0712504949 | 3.87E-06 | 2.07E-06 | mr1042 | 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 |
| vg0712504949 | NA | 7.62E-06 | mr1043 | 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 |
| vg0712504949 | NA | 7.80E-06 | mr1043 | 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 |
| vg0712504949 | NA | 7.20E-06 | mr1502 | 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 |