Variant ID: vg0808034898 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 8034898 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 94. )
GCAACGCAGCTACACCACTCGTCCAAGCCATGTTCTTCAATAACAATGGCCTGAGTTCATTTGATGCTGCCGAGATCTTCGACAAGCTAAGAATTGCTCC[G/A]
GATACATATTTTAATAATATCAAGGAAGCTGGAAGAATGGGAGCAGGCCTGGCATTGGCGATGACCAAGTCCTTGTACCCGAAGATTGATATTGACGCCA
TGGCGTCAATATCAATCTTCGGGTACAAGGACTTGGTCATCGCCAATGCCAGGCCTGCTCCCATTCTTCCAGCTTCCTTGATATTATTAAAATATGTATC[C/T]
GGAGCAATTCTTAGCTTGTCGAAGATCTCGGCAGCATCAAATGAACTCAGGCCATTGTTATTGAAGAACATGGCTTGGACGAGTGGTGTAGCTGCGTTGC
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 57.20% | 40.50% | 0.17% | 2.09% | NA |
All Indica | 2759 | 82.60% | 17.20% | 0.18% | 0.00% | NA |
All Japonica | 1512 | 11.10% | 82.30% | 0.13% | 6.48% | NA |
Aus | 269 | 48.00% | 52.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 92.60% | 7.40% | 0.00% | 0.00% | NA |
Indica II | 465 | 53.80% | 45.40% | 0.86% | 0.00% | NA |
Indica III | 913 | 88.10% | 11.90% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 85.80% | 14.10% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 3.00% | 94.00% | 0.00% | 3.00% | NA |
Tropical Japonica | 504 | 21.40% | 75.80% | 0.00% | 2.78% | NA |
Japonica Intermediate | 241 | 15.40% | 58.50% | 0.83% | 25.31% | NA |
VI/Aromatic | 96 | 77.10% | 22.90% | 0.00% | 0.00% | NA |
Intermediate | 90 | 61.10% | 36.70% | 1.11% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0808034898 | G -> A | LOC_Os08g13500.1 | synonymous_variant ; p.Pro638Pro; LOW | synonymous_codon | Average:43.54; most accessible tissue: Minghui63 flag leaf, score: 63.086 | N | N | N | N |
vg0808034898 | G -> DEL | LOC_Os08g13500.1 | N | frameshift_variant | Average:43.54; most accessible tissue: Minghui63 flag leaf, score: 63.086 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0808034898 | 5.29E-06 | NA | mr1480_2 | 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 |
vg0808034898 | NA | 6.28E-06 | mr1863_2 | 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 |
vg0808034898 | 5.85E-06 | 5.65E-21 | mr1968_2 | 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 |
vg0808034898 | 4.81E-06 | 8.73E-08 | mr1968_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 |