Search for Variation information by Variation ID:
Detailed information for vg0413415787:
| Variant ID: vg0413415787 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 13415787 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 113. )
Flanking Sequence (100 bp) in Reference Genome:
AAACAAAATAAGGGAAATCAAATAACATTTGAGAATGGTAAGCTCATTTTACCTCTTTTTCGCTGCCCGAGTGGATCGCAAGTTGTATTGTGTGGGTTGC[A/G]
TCCCCTGAGGCGCGTCGGGAAGCTGCGACATGTCTATCTCCTCAGCGTCTGGTGCGACGTAGTCCTCATCCTCCTCATCCTCATCGTCATCGTCGTCGCT
Reverse complement sequence
AGCGACGACGATGACGATGAGGATGAGGAGGATGAGGACTACGTCGCACCAGACGCTGAGGAGATAGACATGTCGCAGCTTCCCGACGCGCCTCAGGGGA[T/C]
GCAACCCACACAATACAACTTGCGATCCACTCGGGCAGCGAAAAAGAGGTAAAATGAGCTTACCATTCTCAAATGTTATTTGATTTCCCTTATTTTGTTT
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 | 62.80% | 22.90% | 7.28% | 6.94% | NA |
| All Indica | 2759 | 83.10% | 4.10% | 6.89% | 5.91% | NA |
| All Japonica | 1512 | 24.00% | 60.10% | 8.66% | 7.28% | NA |
| Aus | 269 | 94.80% | 3.00% | 2.23% | 0.00% | NA |
| Indica I | 595 | 67.70% | 11.60% | 9.08% | 11.60% | NA |
| Indica II | 465 | 75.10% | 2.80% | 19.14% | 3.01% | NA |
| Indica III | 913 | 96.20% | 0.80% | 0.77% | 2.30% | NA |
| Indica Intermediate | 786 | 84.40% | 3.10% | 5.09% | 7.51% | NA |
| Temperate Japonica | 767 | 3.50% | 93.20% | 1.43% | 1.83% | NA |
| Tropical Japonica | 504 | 53.80% | 16.30% | 17.06% | 12.90% | NA |
| Japonica Intermediate | 241 | 27.00% | 46.10% | 14.11% | 12.86% | NA |
| VI/Aromatic | 96 | 14.60% | 29.20% | 10.42% | 45.83% | NA |
| Intermediate | 90 | 50.00% | 30.00% | 7.78% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0413415787 | A -> DEL | LOC_Os04g23470.1 | N | frameshift_variant | Average:14.39; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
| vg0413415787 | A -> G | LOC_Os04g23470.1 | missense_variant ; p.Met1507Thr; MODERATE | nonsynonymous_codon ; M1507T | Average:14.39; most accessible tissue: Zhenshan97 panicle, score: 28.447 | benign  |
-0.525 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0413415787 | NA | 9.22E-06 | mr1029 | Jap_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 |
| vg0413415787 | NA | 5.61E-06 | mr1047 | Jap_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 |
| vg0413415787 | NA | 4.35E-09 | mr1502 | Jap_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 |
| vg0413415787 | NA | 4.15E-08 | mr1543 | Jap_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 |
| vg0413415787 | NA | 5.42E-07 | mr1977 | 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 |