Search for Variation information by Variation ID:
Detailed information for vg0716168165:
| Variant ID: vg0716168165 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 16168165 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 318. )
Flanking Sequence (100 bp) in Reference Genome:
GGGTGTGGGCCATCTCGCAACTTTCCTTGTCACACGTGACGGCTTGCTTGATGTCACTCCGTAGGGATATGACTCCTCGGGGACCGGGCATCTTCATCAT[C/G]
ATGTAGGTATAGTGCGGGACGGCCATGAACTTGGCTAACGCCGGGCGTCCGAGTATGACATGATATGCTGTCTCGAAGTCAGCGACCTCGAAACAAATGT
Reverse complement sequence
ACATTTGTTTCGAGGTCGCTGACTTCGAGACAGCATATCATGTCATACTCGGACGCCCGGCGTTAGCCAAGTTCATGGCCGTCCCGCACTATACCTACAT[G/C]
ATGATGAAGATGCCCGGTCCCCGAGGAGTCATATCCCTACGGAGTGACATCAAGCAAGCCGTCACGTGTGACAAGGAAAGTTGCGAGATGGCCCACACCC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.90% | 1.60% | 0.57% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.20% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 93.90% | 4.50% | 1.59% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.10% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 90.10% | 7.70% | 2.22% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 0.80% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 2.10% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0716168165 | C -> G | LOC_Os07g27720.1 | missense_variant ; p.Met722Ile; MODERATE | nonsynonymous_codon ; M722I | Average:54.933; most accessible tissue: Zhenshan97 panicle, score: 77.482 | benign  |
0.119 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0716168165 | 3.84E-06 | 1.88E-07 | mr1060_2 | 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 |