Search for Variation information by Variation ID:
Detailed information for vg0800164349:
| Variant ID: vg0800164349 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164349 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 80. )
Flanking Sequence (100 bp) in Reference Genome:
TGGGAACTCCTAGAGTTGGCACGTCAGCCCCGGCCAGATACATTCCAGGCTTCATCGTAACCATTGCAAGGAAGTCATTGTATGAAGAAGGGCAGACGTG[T/C]
AGCATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCGCGTCATCGGCAGACAACCGTGCTCCCACGATGCATC
Reverse complement sequence
GATGCATCGTGGGAGCACGGTTGTCTGCCGATGACGCGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGCT[A/G]
CACGTCTGCCCTTCTTCATACAATGACTTCCTTGCAATGGTTACGATGAAGCCTGGAATGTATCTGGCCGGGGCTGACGTGCCAACTCTAGGAGTTCCCA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.20% | 29.20% | 19.28% | 19.30% | NA |
| All Indica | 2759 | 5.30% | 45.40% | 27.36% | 21.96% | NA |
| All Japonica | 1512 | 87.40% | 0.90% | 1.12% | 10.58% | NA |
| Aus | 269 | 1.90% | 37.90% | 39.03% | 21.19% | NA |
| Indica I | 595 | 11.30% | 31.30% | 38.15% | 19.33% | NA |
| Indica II | 465 | 2.40% | 51.40% | 29.89% | 16.34% | NA |
| Indica III | 913 | 2.60% | 50.70% | 20.37% | 26.29% | NA |
| Indica Intermediate | 786 | 5.50% | 46.40% | 25.83% | 22.26% | NA |
| Temperate Japonica | 767 | 97.10% | 0.50% | 0.52% | 1.83% | NA |
| Tropical Japonica | 504 | 72.20% | 1.60% | 2.18% | 24.01% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.40% | 0.83% | 10.37% | NA |
| VI/Aromatic | 96 | 13.50% | 2.10% | 17.71% | 66.67% | NA |
| Intermediate | 90 | 40.00% | 13.30% | 18.89% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164349 | T -> C | LOC_Os08g01250.1 | synonymous_variant ; p.Leu45Leu; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800164349 | T -> C | LOC_Os08g01250.1 | synonymous_variant ; p.Leu45Leu; LOW | nonsynonymous_codon ; L45P | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-0.289 |
TOLERATED | 0.22 |
| vg0800164349 | T -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0800164349 | NA | 1.23E-14 | mr1653 | 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 |
| vg0800164349 | NA | 2.12E-10 | mr1746 | 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 |
| vg0800164349 | NA | 3.23E-18 | mr1746_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 |