Variant ID: vg0211784502 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 11784502 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 222. )
TGTTGAATCTACAGATTTACAGATTCTGAATAATTCTTACATCACCATTGTGCCAAAAAAAAACTTCTCCAGAAACAGTTAATGATTTCAGGCCAATTTC[T/C]
CTAATGGGTTTGAGCCTTAAGTTCCTTACCAAATTGATGGCTGATAGATTGCAAGGTGTGATTCTCAAAGTGGTTAGTGAAAACCAATATGGATTCATCA
TGATGAATCCATATTGGTTTTCACTAACCACTTTGAGAATCACACCTTGCAATCTATCAGCCATCAATTTGGTAAGGAACTTAAGGCTCAAACCCATTAG[A/G]
GAAATTGGCCTGAAATCATTAACTGTTTCTGGAGAAGTTTTTTTTTGGCACAATGGTGATGTAAGAATTATTCAGAATCTGTAAATCTGTAGATTCAACA
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 43.00% | 16.60% | 5.99% | 34.41% | NA |
All Indica | 2759 | 10.60% | 22.80% | 9.64% | 56.94% | NA |
All Japonica | 1512 | 98.30% | 0.10% | 0.13% | 1.46% | NA |
Aus | 269 | 39.40% | 53.50% | 3.72% | 3.35% | NA |
Indica I | 595 | 6.10% | 19.30% | 5.55% | 69.08% | NA |
Indica II | 465 | 8.40% | 34.20% | 6.88% | 50.54% | NA |
Indica III | 913 | 13.80% | 20.30% | 14.35% | 51.59% | NA |
Indica Intermediate | 786 | 11.70% | 21.60% | 8.91% | 57.76% | NA |
Temperate Japonica | 767 | 99.00% | 0.10% | 0.00% | 0.91% | NA |
Tropical Japonica | 504 | 97.40% | 0.20% | 0.20% | 2.18% | NA |
Japonica Intermediate | 241 | 97.90% | 0.00% | 0.41% | 1.66% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 58.90% | 8.90% | 5.56% | 26.67% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0211784502 | T -> DEL | LOC_Os02g20010.1 | N | frameshift_variant | Average:14.621; most accessible tissue: Callus, score: 35.53 | N | N | N | N |
vg0211784502 | T -> C | LOC_Os02g20010.1 | synonymous_variant ; p.Ser784Ser; LOW | synonymous_codon | Average:14.621; most accessible tissue: Callus, score: 35.53 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0211784502 | NA | 3.13E-06 | mr1538 | Ind_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 |
vg0211784502 | 5.24E-06 | 6.18E-07 | mr1547 | 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 |
vg0211784502 | 1.61E-06 | 6.46E-09 | mr1547 | 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 |
vg0211784502 | 3.29E-08 | 3.69E-14 | mr1709 | 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 |
vg0211784502 | 3.46E-07 | 5.31E-12 | mr1709 | Ind_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 |
vg0211784502 | NA | 9.30E-07 | mr1547_2 | Ind_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 |
vg0211784502 | 8.08E-07 | 2.31E-15 | mr1709_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 |
vg0211784502 | NA | 8.68E-13 | mr1709_2 | Ind_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 |