Variant ID: vg0432427836 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 32427836 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.84, C: 0.15, others allele: 0.00, population size: 68. )
TAAAGATCGATCTTTAGTCCCGGTTGGTAATACCAACCGGGACTAAAGATGTAGCGCCCGTTCCGTCGTGGCGCCTAGCGGGAAAATTATCTCCTAAAAA[T/C]
CCTAATTGCGAAATTTGTTTCTTTGCTTGTTGTCTAGTGTCCGTGCCATCTCAAGATCTCAATCCCCGATCTATCGTCGAGTTCAATTCCGAATCCAAAT
ATTTGGATTCGGAATTGAACTCGACGATAGATCGGGGATTGAGATCTTGAGATGGCACGGACACTAGACAACAAGCAAAGAAACAAATTTCGCAATTAGG[A/G]
TTTTTAGGAGATAATTTTCCCGCTAGGCGCCACGACGGAACGGGCGCTACATCTTTAGTCCCGGTTGGTATTACCAACCGGGACTAAAGATCGATCTTTA
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 | 69.60% | 3.20% | 5.16% | 22.05% | NA |
All Indica | 2759 | 71.30% | 0.20% | 3.33% | 25.19% | NA |
All Japonica | 1512 | 77.70% | 9.30% | 7.54% | 5.42% | NA |
Aus | 269 | 20.10% | 1.10% | 1.49% | 77.32% | NA |
Indica I | 595 | 91.90% | 0.00% | 0.17% | 7.90% | NA |
Indica II | 465 | 73.80% | 0.60% | 2.37% | 23.23% | NA |
Indica III | 913 | 50.80% | 0.00% | 7.89% | 41.29% | NA |
Indica Intermediate | 786 | 78.00% | 0.30% | 1.02% | 20.74% | NA |
Temperate Japonica | 767 | 78.10% | 12.90% | 8.74% | 0.26% | NA |
Tropical Japonica | 504 | 75.60% | 2.00% | 7.34% | 15.08% | NA |
Japonica Intermediate | 241 | 80.90% | 13.30% | 4.15% | 1.66% | NA |
VI/Aromatic | 96 | 25.00% | 0.00% | 32.29% | 42.71% | NA |
Intermediate | 90 | 74.40% | 4.40% | 3.33% | 17.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0432427836 | T -> C | LOC_Os04g54510.1 | upstream_gene_variant ; 2218.0bp to feature; MODIFIER | silent_mutation | Average:42.145; most accessible tissue: Zhenshan97 flower, score: 63.345 | N | N | N | N |
vg0432427836 | T -> C | LOC_Os04g54500.1 | downstream_gene_variant ; 3839.0bp to feature; MODIFIER | silent_mutation | Average:42.145; most accessible tissue: Zhenshan97 flower, score: 63.345 | N | N | N | N |
vg0432427836 | T -> C | LOC_Os04g54520.1 | downstream_gene_variant ; 2193.0bp to feature; MODIFIER | silent_mutation | Average:42.145; most accessible tissue: Zhenshan97 flower, score: 63.345 | N | N | N | N |
vg0432427836 | T -> C | LOC_Os04g54510-LOC_Os04g54520 | intergenic_region ; MODIFIER | silent_mutation | Average:42.145; most accessible tissue: Zhenshan97 flower, score: 63.345 | N | N | N | N |
vg0432427836 | T -> DEL | N | N | silent_mutation | Average:42.145; most accessible tissue: Zhenshan97 flower, score: 63.345 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0432427836 | 6.33E-10 | 1.03E-12 | Grain_weight | All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |