Variant ID: vg0434912939 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 34912939 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.03, others allele: 0.00, population size: 109. )
CTGGCCTGCCTGTCGTTCTTCCTTTTAATCATCATTAGTGTTCTATTTGGTGTTTTATTAACAGTTTTTATATGTCGTATCAACCGCCACCACTCTACTC[T/C]
TTTATAGGCTTGTTACTTAAATTATCTCGTCATGTGTTTTAGATGGTTTTTTCTTTCGATAGTCTTTATTTTTATCACATTTTTCAGTTATTTATAAATT
AATTTATAAATAACTGAAAAATGTGATAAAAATAAAGACTATCGAAAGAAAAAACCATCTAAAACACATGACGAGATAATTTAAGTAACAAGCCTATAAA[A/G]
GAGTAGAGTGGTGGCGGTTGATACGACATATAAAAACTGTTAATAAAACACCAAATAGAACACTAATGATGATTAAAAGGAAGAACGACAGGCAGGCCAG
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 | 84.70% | 14.30% | 0.99% | 0.00% | NA |
All Indica | 2759 | 81.40% | 17.00% | 1.67% | 0.00% | NA |
All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Aus | 269 | 37.90% | 62.10% | 0.00% | 0.00% | NA |
Indica I | 595 | 97.00% | 2.20% | 0.84% | 0.00% | NA |
Indica II | 465 | 52.30% | 46.20% | 1.51% | 0.00% | NA |
Indica III | 913 | 87.10% | 11.30% | 1.64% | 0.00% | NA |
Indica Intermediate | 786 | 80.20% | 17.40% | 2.42% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 72.90% | 27.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 85.60% | 13.30% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0434912939 | T -> C | LOC_Os04g58710.1 | upstream_gene_variant ; 2278.0bp to feature; MODIFIER | silent_mutation | Average:32.518; most accessible tissue: Minghui63 root, score: 50.524 | N | N | N | N |
vg0434912939 | T -> C | LOC_Os04g58720.1 | upstream_gene_variant ; 2852.0bp to feature; MODIFIER | silent_mutation | Average:32.518; most accessible tissue: Minghui63 root, score: 50.524 | N | N | N | N |
vg0434912939 | T -> C | LOC_Os04g58710-LOC_Os04g58720 | intergenic_region ; MODIFIER | silent_mutation | Average:32.518; most accessible tissue: Minghui63 root, score: 50.524 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0434912939 | NA | 2.58E-06 | mr1075 | 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 |
vg0434912939 | NA | 5.89E-06 | mr1149 | 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 |
vg0434912939 | NA | 1.18E-06 | mr1441 | 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 |
vg0434912939 | NA | 1.40E-12 | mr1565 | 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 |