Search for Variation information by Variation ID:
Detailed information for vg0627002372:
| Variant ID: vg0627002372 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 27002372 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
CATGTCACATGAAAAAAAATGGGTCGAAGAACTCCCATCAGTACTATGGGCCGTACGCACCACACCGACAACGTCTAATAAGGAAACACCCTTCTTCCTC[G/A]
TGTACGGCTCCGAGGCCATGCTCCCCAACGAGCTACGACATCAGAGTACACGAGTACAGAAGCACTCCGACGAGGACCAGGTGGAGCAGCGAGACATCGA
Reverse complement sequence
TCGATGTCTCGCTGCTCCACCTGGTCCTCGTCGGAGTGCTTCTGTACTCGTGTACTCTGATGTCGTAGCTCGTTGGGGAGCATGGCCTCGGAGCCGTACA[C/T]
GAGGAAGAAGGGTGTTTCCTTATTAGACGTTGTCGGTGTGGTGCGTACGGCCCATAGTACTGATGGGAGTTCTTCGACCCATTTTTTTTCATGTGACATG
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 | 87.60% | 10.90% | 1.48% | 0.00% | NA |
| All Indica | 2759 | 98.60% | 1.10% | 0.29% | 0.00% | NA |
| All Japonica | 1512 | 65.00% | 31.10% | 3.90% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.00% | 0.84% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.00% | 0.60% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 75.20% | 18.60% | 6.13% | 0.00% | NA |
| Tropical Japonica | 504 | 53.40% | 46.20% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 56.80% | 39.00% | 4.15% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 7.80% | 3.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0627002372 | G -> A | LOC_Os06g44730.1 | missense_variant ; p.Val971Met; MODERATE | nonsynonymous_codon ; V971M | Average:33.392; most accessible tissue: Zhenshan97 panicle, score: 43.098 | benign  |
0.93 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0627002372 | 2.80E-06 | 1.11E-08 | mr1554 | 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 |