Variant ID: vg0807428797 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 7428797 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.07, others allele: 0.00, population size: 108. )
CGCGACCGACGCGAACCTGATTTCCAGATTAAGCCCTTCGCACATTTCTCTGAACTTGTTAGAGTCGAACTGCTTGCCGTTGTCAGTGATGAACTCTTTT[G/A]
GCACTCCGAAACGGCAAATAATGTTTTTCCATACAAACTTCTGTACTGCTGCCGAAGTGAATGCTCCGAGGGGTTCGGCCTCAATCCATCGGGAGAAGTA
TACTTCTCCCGATGGATTGAGGCCGAACCCCTCGGAGCATTCACTTCGGCAGCAGTACAGAAGTTTGTATGGAAAAACATTATTTGCCGTTTCGGAGTGC[C/T]
AAAAGAGTTCATCACTGACAACGGCAAGCAGTTCGACTCTAACAAGTTCAGAGAAATGTGCGAAGGGCTTAATCTGGAAATCAGGTTCGCGTCGGTCGCG
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 | 55.40% | 43.90% | 0.25% | 0.51% | NA |
All Indica | 2759 | 28.80% | 70.00% | 0.29% | 0.87% | NA |
All Japonica | 1512 | 97.90% | 1.80% | 0.26% | 0.00% | NA |
Aus | 269 | 77.00% | 23.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 15.30% | 81.70% | 0.34% | 2.69% | NA |
Indica II | 465 | 49.50% | 49.70% | 0.00% | 0.86% | NA |
Indica III | 913 | 22.70% | 76.80% | 0.33% | 0.22% | NA |
Indica Intermediate | 786 | 34.00% | 65.40% | 0.38% | 0.25% | NA |
Temperate Japonica | 767 | 96.90% | 2.60% | 0.52% | 0.00% | NA |
Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 77.10% | 22.90% | 0.00% | 0.00% | NA |
Intermediate | 90 | 66.70% | 33.30% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0807428797 | G -> A | LOC_Os08g12550.1 | missense_variant ; p.Pro295Leu; MODERATE | nonsynonymous_codon ; P295L | Average:43.929; most accessible tissue: Minghui63 young leaf, score: 75.937 | benign | 0.945 | TOLERATED | 0.07 |
vg0807428797 | G -> DEL | LOC_Os08g12550.1 | N | frameshift_variant | Average:43.929; most accessible tissue: Minghui63 young leaf, score: 75.937 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0807428797 | NA | 6.04E-06 | mr1577 | 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 |