Search for Variation information by Variation ID:
Detailed information for vg0417122308:
| Variant ID: vg0417122308 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17122308 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 354. )
Flanking Sequence (100 bp) in Reference Genome:
GACCTCAACAAATCTTGTCCCAAAGACCCTTTTGGGTTACCTCGCATTGACCAGGTGGTTGACTCAACAGCCGGCTGCGAGTTACTCAGCTTCTTGGACT[G/A]
TTACTCGGGATATCATCAGATCCGACTAAAAGAATCCGACTGCTTGAAGACCTCGTTTATTACGCCCTTTGGGGCCTACTGCTACATCACCATGCTCTTT
Reverse complement sequence
AAAGAGCATGGTGATGTAGCAGTAGGCCCCAAAGGGCGTAATAAACGAGGTCTTCAAGCAGTCGGATTCTTTTAGTCGGATCTGATGATATCCCGAGTAA[C/T]
AGTCCAAGAAGCTGAGTAACTCGCAGCCGGCTGTTGAGTCAACCACCTGGTCAATGCGAGGTAACCCAAAAGGGTCTTTGGGACAAGATTTGTTGAGGTC
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 | 97.20% | 0.60% | 2.16% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 0.00% | 1.09% | 0.00% | NA |
| All Japonica | 1512 | 93.50% | 1.90% | 4.63% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.10% | 0.00% | 4.87% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 89.00% | 2.90% | 8.08% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.20% | 2.50% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0417122308 | G -> A | LOC_Os04g28880.1 | missense_variant ; p.Cys1104Tyr; MODERATE | nonsynonymous_codon ; C1104Y | Average:32.937; most accessible tissue: Minghui63 panicle, score: 59.629 | probably damaging  |
2.491 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417122308 | NA | 2.53E-10 | Awn_length | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0417122308 | 9.53E-06 | 2.05E-12 | mr1549 | 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 |
| vg0417122308 | NA | 3.54E-09 | mr1757 | 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 |
| vg0417122308 | NA | 8.84E-08 | mr1549_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 |
| vg0417122308 | NA | 1.08E-08 | mr1757_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 |