Search for Variation information by Variation ID:
Detailed information for vg0715473397:
| Variant ID: vg0715473397 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 15473397 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGTCGGACCGGCCATCTGGCTGGTCGGACCGGCCGTGAACACCGCCCCGTCGGTTTTAGACCCTATTGGATCTACAGGAGGTTGATCAGCAGTGGTATAG[G/A]
CTTTATCCTTTAATGTGTAATCATCCATAAAAGAACCTAGCCTACTCCTTAAAAACCCATCAACTTTTTCCTTAAACATCATATCTAATCTATCTTTAAA
Reverse complement sequence
TTTAAAGATAGATTAGATATGATGTTTAAGGAAAAAGTTGATGGGTTTTTAAGGAGTAGGCTAGGTTCTTTTATGGATGATTACACATTAAAGGATAAAG[C/T]
CTATACCACTGCTGATCAACCTCCTGTAGATCCAATAGGGTCTAAAACCGACGGGGCGGTGTTCACGGCCGGTCCGACCAGCCAGATGGCCGGTCCGACC
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 | 90.50% | 0.30% | 4.17% | 5.04% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.04% | NA |
| All Japonica | 1512 | 71.20% | 0.80% | 12.50% | 15.54% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.00% | 0.22% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 84.20% | 1.20% | 5.74% | 8.87% | NA |
| Tropical Japonica | 504 | 52.80% | 0.60% | 19.05% | 27.58% | NA |
| Japonica Intermediate | 241 | 68.00% | 0.00% | 20.33% | 11.62% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 94.40% | 0.00% | 5.56% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0715473397 | G -> DEL | LOC_Os07g26780.1 | N | frameshift_variant | Average:16.202; most accessible tissue: Minghui63 flag leaf, score: 30.104 | N | N | N | N |
| vg0715473397 | G -> A | LOC_Os07g26780.1 | missense_variant ; p.Ala126Val; MODERATE | nonsynonymous_codon ; A126V | Average:16.202; most accessible tissue: Minghui63 flag leaf, score: 30.104 | benign  |
1.453 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0715473397 | NA | 6.79E-07 | mr1062 | 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 |
| vg0715473397 | 3.22E-06 | 3.22E-06 | mr1346 | 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 |
| vg0715473397 | 7.64E-06 | 7.63E-06 | mr1456 | 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 |