Search for Variation information by Variation ID:
Detailed information for vg1004375218:
| Variant ID: vg1004375218 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4375218 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 116. )
Flanking Sequence (100 bp) in Reference Genome:
GATTGCGGAAGACGACGGAGAAGAGCGCACCCATCGCAGATGCATGTCATATGGAGAATATGCATCCACACCAACCGATGCTGGAGCGAAGCTATCGGCT[A/G]
AGCTACTCAAGGACTGGTTCTGCAGCTTCTACGAAGGTTTTAAGAAAGATGCACGAATCTGGTTTCCTTATGAAGACTCAGCAAACCTTGAACTTCCATC
Reverse complement sequence
GATGGAAGTTCAAGGTTTGCTGAGTCTTCATAAGGAAACCAGATTCGTGCATCTTTCTTAAAACCTTCGTAGAAGCTGCAGAACCAGTCCTTGAGTAGCT[T/C]
AGCCGATAGCTTCGCTCCAGCATCGGTTGGTGTGGATGCATATTCTCCATATGACATGCATCTGCGATGGGTGCGCTCTTCTCCGTCGTCTTCCGCAATC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.20% | 27.10% | 0.28% | 43.46% | NA |
| All Indica | 2759 | 19.00% | 26.80% | 0.33% | 53.82% | NA |
| All Japonica | 1512 | 53.30% | 15.20% | 0.00% | 31.48% | NA |
| Aus | 269 | 4.10% | 91.80% | 0.74% | 3.35% | NA |
| Indica I | 595 | 35.10% | 42.50% | 0.00% | 22.35% | NA |
| Indica II | 465 | 20.20% | 24.90% | 0.22% | 54.62% | NA |
| Indica III | 913 | 3.10% | 20.80% | 0.33% | 75.79% | NA |
| Indica Intermediate | 786 | 24.70% | 23.00% | 0.64% | 51.65% | NA |
| Temperate Japonica | 767 | 79.80% | 9.60% | 0.00% | 10.56% | NA |
| Tropical Japonica | 504 | 18.70% | 15.70% | 0.00% | 65.67% | NA |
| Japonica Intermediate | 241 | 41.50% | 32.00% | 0.00% | 26.56% | NA |
| VI/Aromatic | 96 | 11.50% | 37.50% | 2.08% | 48.96% | NA |
| Intermediate | 90 | 27.80% | 31.10% | 0.00% | 41.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1004375218 | A -> G | LOC_Os10g08080.1 | missense_variant ; p.Lys315Glu; MODERATE | nonsynonymous_codon ; K315E | Average:32.208; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 | benign  |
-0.485 |
TOLERATED | 1.00 |
| vg1004375218 | A -> DEL | LOC_Os10g08080.1 | N | frameshift_variant | Average:32.208; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004375218 | NA | 2.55E-06 | Yield | 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 |
| vg1004375218 | 7.29E-06 | 7.69E-07 | mr1768 | 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 |
| vg1004375218 | 3.22E-06 | NA | mr1768_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 |
| vg1004375218 | 3.13E-06 | 1.40E-07 | mr1768_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 |