Variant ID: vg0609007802 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 9007802 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )
CATCTCCACTTTCCTCCTCGCTAGCCCCCTCAACATTGGCCTCAACCTCTTCATCACTTTGAGCGTAATCCTCTCTGCTCGATTCCTCAGGCTCACTCAC[G/A]
GGATCAGGCGCACGACGACCATGACGAGTGCGGGGAGGCATCACTGAAAAAATAGGAGCAAAGGATATATAAGCAATAATTTTAGAAACCACATAGTGAA
TTCACTATGTGGTTTCTAAAATTATTGCTTATATATCCTTTGCTCCTATTTTTTCAGTGATGCCTCCCCGCACTCGTCATGGTCGTCGTGCGCCTGATCC[C/T]
GTGAGTGAGCCTGAGGAATCGAGCAGAGAGGATTACGCTCAAAGTGATGAAGAGGTTGAGGCCAATGTTGAGGGGGCTAGCGAGGAGGAAAGTGGAGATG
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 | 77.80% | 22.10% | 0.06% | 0.00% | NA |
All Indica | 2759 | 91.60% | 8.40% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 49.30% | 50.50% | 0.20% | 0.00% | NA |
Aus | 269 | 92.20% | 7.80% | 0.00% | 0.00% | NA |
Indica I | 595 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
Indica II | 465 | 83.00% | 17.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 89.40% | 10.60% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 76.00% | 23.70% | 0.26% | 0.00% | NA |
Tropical Japonica | 504 | 15.90% | 83.90% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 34.40% | 65.60% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 70.00% | 30.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0609007802 | G -> A | LOC_Os06g15860.1 | synonymous_variant ; p.Pro14Pro; LOW | synonymous_codon | Average:67.737; most accessible tissue: Minghui63 young leaf, score: 79.896 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0609007802 | NA | 1.43E-06 | mr1087 | Jap_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 |
vg0609007802 | NA | 3.15E-06 | mr1242 | 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 |
vg0609007802 | 2.98E-07 | NA | mr1842 | 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 |
vg0609007802 | NA | 6.64E-12 | mr1871 | 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 |
vg0609007802 | 2.32E-06 | 1.40E-12 | mr1087_2 | Jap_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 |
vg0609007802 | NA | 3.14E-06 | mr1091_2 | Jap_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 |
vg0609007802 | NA | 6.04E-07 | mr1096_2 | Jap_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 |
vg0609007802 | NA | 8.52E-10 | mr1570_2 | Jap_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 |