Variant ID: vg0214439802 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 14439802 |
Reference Allele: T | Alternative Allele: A |
Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 127. )
TAAGAAATACCAACATTCACCAAGGCAGGGGATGAGGTGCTCCACAAGTATGTCACACCCACCGCTACTCCATCCACTCCAAAGGAGGAGCGGTTTTGCA[T/A]
TATGGGAGTGCGAACTCCCAGCGGTGGGTATGGCAAGGGTTTGCTCCGGCCTTTGACAGCAACGGAGAAGGAGGGGGCAGCAGAATCTCGTATCCCTCCA
TGGAGGGATACGAGATTCTGCTGCCCCCTCCTTCTCCGTTGCTGTCAAAGGCCGGAGCAAACCCTTGCCATACCCACCGCTGGGAGTTCGCACTCCCATA[A/T]
TGCAAAACCGCTCCTCCTTTGGAGTGGATGGAGTAGCGGTGGGTGTGACATACTTGTGGAGCACCTCATCCCCTGCCTTGGTGAATGTTGGTATTTCTTA
Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 83.50% | 1.50% | 2.84% | 12.12% | NA |
All Indica | 2759 | 72.40% | 2.40% | 4.82% | 20.41% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 95.90% | 0.70% | 0.37% | 2.97% | NA |
Indica I | 595 | 69.70% | 3.40% | 5.38% | 21.51% | NA |
Indica II | 465 | 83.00% | 0.90% | 3.87% | 12.26% | NA |
Indica III | 913 | 67.40% | 2.10% | 4.93% | 25.63% | NA |
Indica Intermediate | 786 | 73.90% | 2.90% | 4.83% | 18.32% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 95.60% | 2.20% | 0.00% | 2.22% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0214439802 | T -> A | LOC_Os02g24910.1 | missense_variant ; p.Ile57Asn; MODERATE | nonsynonymous_codon ; I57N | Average:41.997; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | probably damaging | 2.422 | DELETERIOUS | 0.04 |
vg0214439802 | T -> DEL | LOC_Os02g24910.1 | N | frameshift_variant | Average:41.997; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0214439802 | 8.90E-07 | 9.43E-06 | mr1242 | 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 |