Variant ID: vg0336012854 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 36012854 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCAAAAATTACTTTAGAGAAGTTGCTTTAAAAACTCATATCAATTAATTTTTAAAATTTAAAAGAATTAATACTCAATTAATTATGCGCTAGCTTATCTT[C/T]
TCAATCTTTTCTTTTCCCCTACTCACAAACACTCTCTTAGTGGCAGGAGGGTTTCGGTAGGGCCCCCTTGAATCGCATGAATAAGAAAACATAGGAATAG
CTATTCCTATGTTTTCTTATTCATGCGATTCAAGGGGGCCCTACCGAAACCCTCCTGCCACTAAGAGAGTGTTTGTGAGTAGGGGAAAAGAAAAGATTGA[G/A]
AAGATAAGCTAGCGCATAATTAATTGAGTATTAATTCTTTTAAATTTTAAAAATTAATTGATATGAGTTTTTAAAGCAACTTCTCTAAAGTAATTTTTGC
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 | 98.50% | 0.90% | 0.59% | 0.00% | NA |
All Indica | 2759 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 95.60% | 2.80% | 1.65% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 95.00% | 2.20% | 2.74% | 0.00% | NA |
Tropical Japonica | 504 | 95.80% | 3.80% | 0.40% | 0.00% | NA |
Japonica Intermediate | 241 | 96.70% | 2.50% | 0.83% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 1.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0336012854 | C -> T | LOC_Os03g63780.1 | upstream_gene_variant ; 1447.0bp to feature; MODIFIER | silent_mutation | Average:29.459; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
vg0336012854 | C -> T | LOC_Os03g63770-LOC_Os03g63780 | intergenic_region ; MODIFIER | silent_mutation | Average:29.459; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0336012854 | 7.21E-07 | 7.21E-07 | mr1924 | Jap_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 |
vg0336012854 | 1.05E-06 | 1.05E-06 | mr1004_2 | Jap_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 |