Search for Variation information by Variation ID:
Detailed information for vg0417064731:
| Variant ID: vg0417064731 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17064731 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 363. )
Flanking Sequence (100 bp) in Reference Genome:
TCCTCGCACCACCAACCTTGTGCCATTACAAAGTCCATTAGCTGGGTCGATATTCCTGAGCAATATGATAGGACAATTAATTTTGAGCTTTAGCATGTGT[G/A]
GAGGCAGTCCATATGGGGTAAGAGTGTTAAGGAATTTTGGGGGATAGTAGTTATGAGGATCATCTTCCGCACTATCAAAGCTGTGATACACCATCTCCTC
Reverse complement sequence
GAGGAGATGGTGTATCACAGCTTTGATAGTGCGGAAGATGATCCTCATAACTACTATCCCCCAAAATTCCTTAACACTCTTACCCCATATGGACTGCCTC[C/T]
ACACATGCTAAAGCTCAAAATTAATTGTCCTATCATATTGCTCAGGAATATCGACCCAGCTAATGGACTTTGTAATGGCACAAGGTTGGTGGTGCGAGGA
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 | 96.00% | 2.40% | 1.61% | 0.00% | NA |
| All Indica | 2759 | 98.00% | 0.40% | 1.59% | 0.00% | NA |
| All Japonica | 1512 | 91.60% | 6.50% | 1.85% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 96.80% | 0.00% | 3.19% | 0.00% | NA |
| Indica II | 465 | 96.60% | 1.10% | 2.37% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.60% | 0.80% | 1.65% | 0.00% | NA |
| Temperate Japonica | 767 | 98.00% | 0.10% | 1.83% | 0.00% | NA |
| Tropical Japonica | 504 | 79.40% | 18.70% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.70% | 1.70% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 4.40% | 3.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0417064731 | G -> A | LOC_Os04g28820.1 | missense_variant ; p.Pro1712Leu; MODERATE | nonsynonymous_codon ; P1712L | Average:51.991; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | benign  |
1.118 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417064731 | NA | 4.79E-06 | mr1076 | 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 |
| vg0417064731 | NA | 7.12E-07 | mr1227 | 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 |
| vg0417064731 | 2.46E-08 | NA | mr1301 | 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 |
| vg0417064731 | 3.08E-07 | NA | mr1410 | 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 |
| vg0417064731 | 6.62E-08 | NA | mr1301_2 | 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 |
| vg0417064731 | 2.59E-07 | NA | mr1410_2 | 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 |
| vg0417064731 | NA | 2.05E-07 | mr1836_2 | 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 |