Variant ID: vg0922495667 (JBrowse) | Variation Type: SNP |
Chromosome: chr09 | Position: 22495667 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 58. )
TCGTCGATAGGTTAAATCTACATTCATCTTTGATTTGGATTTTCTTTTTAGTCTAGATAGATACTCACTTCTTCTCATATTGATCATCATATAAGAAAAT[G/A]
CACCAAGACTAAGAGCAAGTATAATAGTGAGCTATAAGCCTACTATAAGCTTATGTGGAGGAGAGAGATAACAAAAAATCATGGACGTTGGCTCTCAGAG
CTCTGAGAGCCAACGTCCATGATTTTTTGTTATCTCTCTCCTCCACATAAGCTTATAGTAGGCTTATAGCTCACTATTATACTTGCTCTTAGTCTTGGTG[C/T]
ATTTTCTTATATGATGATCAATATGAGAAGAAGTGAGTATCTATCTAGACTAAAAAGAAAATCCAAATCAAAGATGAATGTAGATTTAACCTATCGACGA
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 | 38.10% | 10.70% | 2.20% | 49.05% | NA |
All Indica | 2759 | 4.80% | 18.00% | 2.86% | 74.37% | NA |
All Japonica | 1512 | 99.50% | 0.00% | 0.00% | 0.46% | NA |
Aus | 269 | 8.60% | 0.70% | 8.18% | 82.53% | NA |
Indica I | 595 | 4.90% | 31.60% | 3.36% | 60.17% | NA |
Indica II | 465 | 6.50% | 6.50% | 5.38% | 81.72% | NA |
Indica III | 913 | 2.20% | 15.20% | 1.53% | 81.05% | NA |
Indica Intermediate | 786 | 6.70% | 17.70% | 2.54% | 73.03% | NA |
Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
VI/Aromatic | 96 | 88.50% | 0.00% | 2.08% | 9.38% | NA |
Intermediate | 90 | 61.10% | 6.70% | 1.11% | 31.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0922495667 | G -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0922495667 | G -> A | LOC_Os09g39170.1 | upstream_gene_variant ; 1347.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0922495667 | G -> A | LOC_Os09g39170-LOC_Os09g39180 | intergenic_region ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0922495667 | 1.01E-07 | NA | mr1865 | 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 |
vg0922495667 | 8.57E-09 | 2.49E-11 | mr1865 | 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 |
vg0922495667 | 1.84E-06 | NA | mr1520_2 | 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 |
vg0922495667 | 3.72E-06 | 9.41E-08 | mr1520_2 | 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 |
vg0922495667 | 6.67E-06 | 3.09E-10 | mr1865_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 |
vg0922495667 | NA | 9.86E-06 | mr1968_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 |