Variant ID: vg1221032304 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 21032304 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGGTAAAAGCCGTCTTAGGTATATCTTCCTCTTTAATCCTCAACTGGTGATACCCCGATCGAAGATCGATTTTGGAGAAAACGGTGGCTCCTTTAAGCTG[A/G]
TCAAACAAATCATCAATTCTAGGCAGAGGGTACTTATTCTTGATGGTCACATCATTTAGTGCACGATAATCCATACACATCCTCTGGGTATGATCTTTCT
AGAAAGATCATACCCAGAGGATGTGTATGGATTATCGTGCACTAAATGATGTGACCATCAAGAATAAGTACCCTCTGCCTAGAATTGATGATTTGTTTGA[T/C]
CAGCTTAAAGGAGCCACCGTTTTCTCCAAAATCGATCTTCGATCGGGGTATCACCAGTTGAGGATTAAAGAGGAAGATATACCTAAGACGGCTTTTACCA
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 | 94.80% | 3.20% | 2.01% | 0.00% | NA |
All Indica | 2759 | 92.10% | 4.70% | 3.23% | 0.00% | NA |
All Japonica | 1512 | 99.70% | 0.20% | 0.07% | 0.00% | NA |
Aus | 269 | 92.90% | 5.60% | 1.49% | 0.00% | NA |
Indica I | 595 | 99.20% | 0.50% | 0.34% | 0.00% | NA |
Indica II | 465 | 93.80% | 4.90% | 1.29% | 0.00% | NA |
Indica III | 913 | 86.30% | 7.30% | 6.35% | 0.00% | NA |
Indica Intermediate | 786 | 92.40% | 4.70% | 2.93% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.20% | 0.60% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 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 |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1221032304 | A -> G | LOC_Os12g34650.1 | synonymous_variant ; p.Asp893Asp; LOW | synonymous_codon | Average:41.935; most accessible tissue: Minghui63 flag leaf, score: 67.635 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1221032304 | 5.71E-06 | NA | mr1952 | 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 |
vg1221032304 | 2.94E-06 | 1.07E-06 | mr1952 | Ind_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 |