Variant ID: vg0725460660 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 25460660 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.02, others allele: 0.00, population size: 81. )
GGCTTGCCCATAACCGAGGGCGCGGTTATTCGAATAGATTATACTCTGATCAGAGGTGTACATCTTTACCCACAAGACACATCTTCCTCACGTGTAACCA[T/C]
GTGCCACATACCACCACGGTATATGGATGGAAGATGTGACATAGTTTCCAACCCATCCTAGCCATAGACAAGAGTACCGACCCAACCCCACCTACGGCCG
CGGCCGTAGGTGGGGTTGGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGAAACTATGTCACATCTTCCATCCATATACCGTGGTGGTATGTGGCAC[A/G]
TGGTTACACGTGAGGAAGATGTGTCTTGTGGGTAAAGATGTACACCTCTGATCAGAGTATAATCTATTCGAATAACCGCGCCCTCGGTTATGGGCAAGCC
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 57.20% | 38.90% | 3.75% | 0.17% | NA |
All Indica | 2759 | 91.80% | 6.00% | 2.10% | 0.11% | NA |
All Japonica | 1512 | 0.10% | 99.90% | 0.00% | 0.00% | NA |
Aus | 269 | 49.40% | 5.60% | 43.12% | 1.86% | NA |
Indica I | 595 | 87.70% | 9.20% | 2.86% | 0.17% | NA |
Indica II | 465 | 92.30% | 7.30% | 0.43% | 0.00% | NA |
Indica III | 913 | 96.30% | 1.10% | 2.63% | 0.00% | NA |
Indica Intermediate | 786 | 89.30% | 8.50% | 1.91% | 0.25% | NA |
Temperate Japonica | 767 | 0.10% | 99.90% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 0.00% | 100.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 4.20% | 95.80% | 0.00% | 0.00% | NA |
Intermediate | 90 | 33.30% | 63.30% | 3.33% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0725460660 | T -> DEL | N | N | silent_mutation | Average:21.188; most accessible tissue: Minghui63 young leaf, score: 27.355 | N | N | N | N |
vg0725460660 | T -> C | LOC_Os07g42550.1 | upstream_gene_variant ; 989.0bp to feature; MODIFIER | silent_mutation | Average:21.188; most accessible tissue: Minghui63 young leaf, score: 27.355 | N | N | N | N |
vg0725460660 | T -> C | LOC_Os07g42540.1 | downstream_gene_variant ; 2737.0bp to feature; MODIFIER | silent_mutation | Average:21.188; most accessible tissue: Minghui63 young leaf, score: 27.355 | N | N | N | N |
vg0725460660 | T -> C | LOC_Os07g42550-LOC_Os07g42560 | intergenic_region ; MODIFIER | silent_mutation | Average:21.188; most accessible tissue: Minghui63 young leaf, score: 27.355 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0725460660 | NA | 1.24E-14 | mr1751 | 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 |
vg0725460660 | NA | 1.07E-06 | mr1751 | 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 |