Search for Variation information by Variation ID:
Detailed information for vg0806568875:
| Variant ID: vg0806568875 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 6568875 |
| 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: 281. )
Flanking Sequence (100 bp) in Reference Genome:
CTTGAACTGTTCTCCCGAAGGTGATGTCAAGATGAACCCTGCCCCTGCTCCTTGGTTGTTGAGTGCGCCGTCGAATGCCATTGTCCATGTTTCGCTGTCT[G/A]
TTTGACTGTCTGACCTGTTCTCAGGCATAGTCCAGTCAGCTACAAAATCAGCAAGAACCTGTGGCTTGATAGCTGTTCATGGCATGAAGTGGACATCAAA
Reverse complement sequence
TTTGATGTCCACTTCATGCCATGAACAGCTATCAAGCCACAGGTTCTTGCTGATTTTGTAGCTGACTGGACTATGCCTGAGAACAGGTCAGACAGTCAAA[C/T]
AGACAGCGAAACATGGACAATGGCATTCGACGGCGCACTCAACAACCAAGGAGCAGGGGCAGGGTTCATCTTGACATCACCTTCGGGAGAACAGTTCAAG
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 | 91.90% | 2.80% | 0.53% | 4.78% | NA |
| All Indica | 2759 | 91.30% | 0.00% | 0.87% | 7.87% | NA |
| All Japonica | 1512 | 91.00% | 8.70% | 0.07% | 0.20% | NA |
| Aus | 269 | 98.50% | 0.00% | 0.00% | 1.49% | NA |
| Indica I | 595 | 95.50% | 0.00% | 0.84% | 3.70% | NA |
| Indica II | 465 | 82.60% | 0.00% | 1.94% | 15.48% | NA |
| Indica III | 913 | 90.90% | 0.00% | 0.55% | 8.54% | NA |
| Indica Intermediate | 786 | 93.60% | 0.00% | 0.64% | 5.73% | NA |
| Temperate Japonica | 767 | 85.40% | 14.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 91.70% | 7.90% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 0.00% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0806568875 | G -> A | LOC_Os08g11180.1 | missense_variant ; p.Thr718Ile; MODERATE | nonsynonymous_codon ; T718I | Average:11.072; most accessible tissue: Callus, score: 24.404 | benign  |
0.541 |
TOLERATED | 0.57 |
| vg0806568875 | G -> DEL | LOC_Os08g11180.1 | N | frameshift_variant | Average:11.072; most accessible tissue: Callus, score: 24.404 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0806568875 | NA | 6.25E-07 | mr1648 | 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 |
| vg0806568875 | NA | 8.07E-06 | mr1697 | 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 |
| vg0806568875 | 2.34E-06 | 4.67E-07 | mr1851 | 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 |
| vg0806568875 | NA | 6.01E-06 | mr1296_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 |
| vg0806568875 | NA | 3.40E-07 | mr1358_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 |