Search for Variation information by Variation ID:
Detailed information for vg1004374859:
| Variant ID: vg1004374859 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4374859 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 103. )
Flanking Sequence (100 bp) in Reference Genome:
GGCTGGTCTGGCTATGTGGCGGCATATATGGGCCAAGGGTCTGTTACCCCTCGAGAGCATGTAGCTTTCTTGGTCATGTGGCTGGAAAAGTTCCTCTTTT[G/A]
TGGATCCAGTTGTGGCCCTACAACCAACTGGAAATTTGTGGCCGAAGCCTTTGAATCAAAGAAAGAATTTCCTGTGGGCAAAATCCTTCTCGGCTATCTG
Reverse complement sequence
CAGATAGCCGAGAAGGATTTTGCCCACAGGAAATTCTTTCTTTGATTCAAAGGCTTCGGCCACAAATTTCCAGTTGGTTGTAGGGCCACAACTGGATCCA[C/T]
AAAAGAGGAACTTTTCCAGCCACATGACCAAGAAAGCTACATGCTCTCGAGGGGTAACAGACCCTTGGCCCATATATGCCGCCACATAGCCAGACCAGCC
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 | 40.30% | 16.00% | 0.19% | 43.53% | NA |
| All Indica | 2759 | 29.20% | 16.40% | 0.25% | 54.11% | NA |
| All Japonica | 1512 | 67.60% | 1.10% | 0.07% | 31.22% | NA |
| Aus | 269 | 2.20% | 93.30% | 0.00% | 4.46% | NA |
| Indica I | 595 | 35.60% | 42.40% | 0.17% | 21.85% | NA |
| Indica II | 465 | 35.10% | 10.50% | 0.22% | 54.19% | NA |
| Indica III | 913 | 20.20% | 3.40% | 0.11% | 76.34% | NA |
| Indica Intermediate | 786 | 31.40% | 15.40% | 0.51% | 52.67% | NA |
| Temperate Japonica | 767 | 89.20% | 0.30% | 0.00% | 10.56% | NA |
| Tropical Japonica | 504 | 32.70% | 2.00% | 0.00% | 65.28% | NA |
| Japonica Intermediate | 241 | 71.80% | 2.10% | 0.41% | 25.73% | NA |
| VI/Aromatic | 96 | 31.20% | 19.80% | 0.00% | 48.96% | NA |
| Intermediate | 90 | 43.30% | 18.90% | 1.11% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1004374859 | G -> A | LOC_Os10g08080.1 | missense_variant ; p.Cys195Tyr; MODERATE | nonsynonymous_codon ; C195Y | Average:35.621; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | benign  |
0.101 |
TOLERATED | 0.12 |
| vg1004374859 | G -> DEL | LOC_Os10g08080.1 | N | frameshift_variant | Average:35.621; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004374859 | 3.36E-06 | 6.16E-07 | mr1094 | 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 |
| vg1004374859 | 3.69E-06 | 2.54E-06 | mr1096 | 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 |
| vg1004374859 | NA | 4.28E-07 | mr1111 | 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 |
| vg1004374859 | 8.30E-06 | 8.30E-06 | mr1144 | 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 |
| vg1004374859 | NA | 5.85E-06 | mr1623_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 |
| vg1004374859 | NA | 7.78E-10 | mr1942_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 |