Variant ID: vg0629462477 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 29462477 |
Reference Allele: A | Alternative Allele: T |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTCAAGAAAAAATTGGCAAATCTCTCTGGATTTTTCATCTTCCTCAGCAATGAAACACTACAACATTGCCAACACTGCAGCGTTACAGGCAAACTGATC[A/T]
GGTAGCTGCACCCATGAATATGCAGATGGATGACTACGAAGTTCATTATGAACAACACATCATTTGCTCAGAACAGCGCAGTGAGGAACAAATTTGACTG
CAGTCAAATTTGTTCCTCACTGCGCTGTTCTGAGCAAATGATGTGTTGTTCATAATGAACTTCGTAGTCATCCATCTGCATATTCATGGGTGCAGCTACC[T/A]
GATCAGTTTGCCTGTAACGCTGCAGTGTTGGCAATGTTGTAGTGTTTCATTGCTGAGGAAGATGAAAAATCCAGAGAGATTTGCCAATTTTTTCTTGAAA
Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 91.60% | 8.40% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 83.70% | 16.30% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0629462477 | A -> T | LOC_Os06g48700.1 | 3_prime_UTR_variant ; 266.0bp to feature; MODIFIER | silent_mutation | Average:49.55; most accessible tissue: Callus, score: 73.89 | N | N | N | N |
vg0629462477 | A -> T | LOC_Os06g48690.1 | upstream_gene_variant ; 1533.0bp to feature; MODIFIER | silent_mutation | Average:49.55; most accessible tissue: Callus, score: 73.89 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0629462477 | 1.66E-06 | 8.93E-06 | mr1595_2 | 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 |