Search for Variation information by Variation ID:
Detailed information for vg0711420958:
| Variant ID: vg0711420958 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 11420958 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 222. )
Flanking Sequence (100 bp) in Reference Genome:
AAGGATTAAATTCGGCCCTCTTATGGACGATTACACGTTAAAGGATAAAGCCTCTATCACTGCTAACCAACCTCCTATAGAACAAACAAATAGTGGAACC[G/A]
ATGGAGCGGCGCATCTAGCCGGTCCGACCGGGCCTGATGGCCGGTCAGACCGTGACATTGCCGTCGGTCCGACCGGCCAAACGGCCGGTCCGACCGGGTA
Reverse complement sequence
TACCCGGTCGGACCGGCCGTTTGGCCGGTCGGACCGACGGCAATGTCACGGTCTGACCGGCCATCAGGCCCGGTCGGACCGGCTAGATGCGCCGCTCCAT[C/T]
GGTTCCACTATTTGTTTGTTCTATAGGAGGTTGGTTAGCAGTGATAGAGGCTTTATCCTTTAACGTGTAATCGTCCATAAGAGGGCCGAATTTAATCCTT
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 | 86.70% | 3.20% | 6.67% | 3.36% | NA |
| All Indica | 2759 | 84.10% | 3.80% | 9.75% | 2.36% | NA |
| All Japonica | 1512 | 99.10% | 0.00% | 0.53% | 0.33% | NA |
| Aus | 269 | 37.90% | 17.10% | 12.64% | 32.34% | NA |
| Indica I | 595 | 90.30% | 0.00% | 8.57% | 1.18% | NA |
| Indica II | 465 | 85.60% | 4.30% | 8.82% | 1.29% | NA |
| Indica III | 913 | 80.10% | 4.30% | 11.72% | 3.94% | NA |
| Indica Intermediate | 786 | 83.30% | 5.70% | 8.91% | 2.04% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.39% | 0.13% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.83% | 1.66% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 3.30% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0711420958 | G -> DEL | LOC_Os07g19300.1 | N | frameshift_variant | Average:34.103; most accessible tissue: Minghui63 flag leaf, score: 47.544 | N | N | N | N |
| vg0711420958 | G -> A | LOC_Os07g19300.1 | missense_variant ; p.Asp135Asn; MODERATE | nonsynonymous_codon ; D135N | Average:34.103; most accessible tissue: Minghui63 flag leaf, score: 47.544 | possibly damaging  |
1.653 |
TOLERATED | 0.12 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0711420958 | 2.11E-07 | 7.81E-07 | mr1119 | 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 |