Search for Variation information by Variation ID:
Detailed information for vg1004369207:
| Variant ID: vg1004369207 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4369207 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.80, G: 0.20, others allele: 0.00, population size: 90. )
Flanking Sequence (100 bp) in Reference Genome:
TTGCTGGCGATAACAACGCTGCGGATGATCTTGGTCAGATGTTGCAGGACGCAAACGAGGACTGTGAAAGTGAAAAGGAGGCCCATAAATTGGAGCGGAT[A/G]
TTAGAGGACCACAGAACGTCGTTGTACCCAGGTTACGAGAAGGGGCACAAAAAGTTGGATACCACTCTGGAGTTCTTACAATGGAAGGCAAAAAATAGTG
Reverse complement sequence
CACTATTTTTTGCCTTCCATTGTAAGAACTCCAGAGTGGTATCCAACTTTTTGTGCCCCTTCTCGTAACCTGGGTACAACGACGTTCTGTGGTCCTCTAA[T/C]
ATCCGCTCCAATTTATGGGCCTCCTTTTCACTTTCACAGTCCTCGTTTGCGTCCTGCAACATCTGACCAAGATCATCCGCAGCGTTGTTATCGCCAGCAA
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 | 43.70% | 10.40% | 0.68% | 45.18% | NA |
| All Indica | 2759 | 34.70% | 10.10% | 0.62% | 54.55% | NA |
| All Japonica | 1512 | 51.90% | 12.30% | 0.73% | 35.12% | NA |
| Aus | 269 | 93.70% | 0.40% | 0.37% | 5.58% | NA |
| Indica I | 595 | 73.80% | 0.20% | 0.67% | 25.38% | NA |
| Indica II | 465 | 29.90% | 14.40% | 0.65% | 55.05% | NA |
| Indica III | 913 | 6.90% | 17.20% | 0.44% | 75.47% | NA |
| Indica Intermediate | 786 | 40.20% | 7.00% | 0.76% | 52.04% | NA |
| Temperate Japonica | 767 | 76.80% | 6.30% | 0.39% | 16.56% | NA |
| Tropical Japonica | 504 | 19.80% | 13.50% | 0.40% | 66.27% | NA |
| Japonica Intermediate | 241 | 39.40% | 29.00% | 2.49% | 29.05% | NA |
| VI/Aromatic | 96 | 31.20% | 19.80% | 0.00% | 48.96% | NA |
| Intermediate | 90 | 47.80% | 7.80% | 3.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1004369207 | A -> G | LOC_Os10g08060.1 | missense_variant ; p.Ile143Met; MODERATE | nonsynonymous_codon ; I143M | Average:31.255; most accessible tissue: Minghui63 flag leaf, score: 45.195 | benign  |
0.019 |
TOLERATED | 1.00 |
| vg1004369207 | A -> DEL | LOC_Os10g08060.1 | N | frameshift_variant | Average:31.255; most accessible tissue: Minghui63 flag leaf, score: 45.195 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004369207 | NA | 1.06E-06 | mr1866_2 | Ind_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 |