Variant ID: vg0505143979 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 5143979 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 89. )
AGTAAATTTCAGAATACAACATATGTAGAAACCAGGGACGGAGCTACCGTTGTTGCACCGGGGTCCTAGGACACCGATGGCCGGAGCTAAATTCCACTTG[A/G]
TACCTATGGTGTAGTTGAATGTGACCCCGGCAAAATTGTTGATTTAAACCCAGCCCATCTGATCATCTTGTATGAGCACAACTACTAATTAAATCTTGGG
CCCAAGATTTAATTAGTAGTTGTGCTCATACAAGATGATCAGATGGGCTGGGTTTAAATCAACAATTTTGCCGGGGTCACATTCAACTACACCATAGGTA[T/C]
CAAGTGGAATTTAGCTCCGGCCATCGGTGTCCTAGGACCCCGGTGCAACAACGGTAGCTCCGTCCCTGGTTTCTACATATGTTGTATTCTGAAATTTACT
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 | 81.60% | 4.60% | 2.86% | 10.96% | NA |
All Indica | 2759 | 86.70% | 7.80% | 2.75% | 2.72% | NA |
All Japonica | 1512 | 88.10% | 0.10% | 0.66% | 11.18% | NA |
Aus | 269 | 15.60% | 0.00% | 15.61% | 68.77% | NA |
Indica I | 595 | 92.30% | 3.00% | 2.86% | 1.85% | NA |
Indica II | 465 | 85.80% | 8.80% | 4.73% | 0.65% | NA |
Indica III | 913 | 88.80% | 8.50% | 0.88% | 1.75% | NA |
Indica Intermediate | 786 | 80.70% | 9.90% | 3.69% | 5.73% | NA |
Temperate Japonica | 767 | 85.30% | 0.10% | 0.52% | 14.08% | NA |
Tropical Japonica | 504 | 89.70% | 0.00% | 0.99% | 9.33% | NA |
Japonica Intermediate | 241 | 93.80% | 0.00% | 0.41% | 5.81% | NA |
VI/Aromatic | 96 | 15.60% | 0.00% | 5.21% | 79.17% | NA |
Intermediate | 90 | 82.20% | 1.10% | 2.22% | 14.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0505143979 | A -> DEL | N | N | silent_mutation | Average:53.361; most accessible tissue: Callus, score: 69.21 | N | N | N | N |
vg0505143979 | A -> G | LOC_Os05g09200.1 | upstream_gene_variant ; 694.0bp to feature; MODIFIER | silent_mutation | Average:53.361; most accessible tissue: Callus, score: 69.21 | N | N | N | N |
vg0505143979 | A -> G | LOC_Os05g09200-LOC_Os05g09210 | intergenic_region ; MODIFIER | silent_mutation | Average:53.361; most accessible tissue: Callus, score: 69.21 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0505143979 | 1.10E-06 | 3.35E-11 | mr1352 | 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 |
vg0505143979 | 5.47E-06 | 4.83E-08 | mr1352 | 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 |
vg0505143979 | 1.23E-06 | 1.23E-06 | mr1905 | 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 |