Search for Variation information by Variation ID:
Detailed information for vg0405200386:
| Variant ID: vg0405200386 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 5200386 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 115. )
Flanking Sequence (100 bp) in Reference Genome:
ATGCCCTTTTTCAAGCTGCTAAAGAAAACCGACAATTTCCAGTGGGGACCCGAAGCGCAAAAAGCCTTTGAAGACTTCAAGAAACTTCTCACCACTCCAC[C/T]
GGTCTTAGCTTCACCACATCCGCAAGAGCCGCTGTTGTTATATGCGTCGGCAACATCTCAGGTTGTGAGCACGGTCCTGGTTGTCGAGCGTGAAGAAGAT
Reverse complement sequence
ATCTTCTTCACGCTCGACAACCAGGACCGTGCTCACAACCTGAGATGTTGCCGACGCATATAACAACAGCGGCTCTTGCGGATGTGGTGAAGCTAAGACC[G/A]
GTGGAGTGGTGAGAAGTTTCTTGAAGTCTTCAAAGGCTTTTTGCGCTTCGGGTCCCCACTGGAAATTGTCGGTTTTCTTTAGCAGCTTGAAAAAGGGCAT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.20% | 2.20% | 5.48% | 5.12% | NA |
| All Indica | 2759 | 93.30% | 2.20% | 2.94% | 1.56% | NA |
| All Japonica | 1512 | 72.80% | 2.80% | 11.44% | 12.96% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.10% | 0.30% | 2.02% | 0.50% | NA |
| Indica II | 465 | 84.90% | 7.10% | 4.09% | 3.87% | NA |
| Indica III | 913 | 95.60% | 0.70% | 2.41% | 1.31% | NA |
| Indica Intermediate | 786 | 92.60% | 2.50% | 3.56% | 1.27% | NA |
| Temperate Japonica | 767 | 69.80% | 0.10% | 5.87% | 24.25% | NA |
| Tropical Japonica | 504 | 70.20% | 7.10% | 22.02% | 0.60% | NA |
| Japonica Intermediate | 241 | 88.00% | 2.10% | 7.05% | 2.90% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 2.20% | 4.44% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0405200386 | C -> DEL | LOC_Os04g09700.1 | N | frameshift_variant | Average:32.078; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 | N | N | N | N |
| vg0405200386 | C -> T | LOC_Os04g09700.1 | missense_variant ; p.Pro34Leu; MODERATE | nonsynonymous_codon ; P34L | Average:32.078; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 | benign  |
1.152 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0405200386 | NA | 5.91E-06 | mr1083 | 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 |
| vg0405200386 | NA | 2.65E-06 | mr1227 | 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 |