Variant ID: vg0607490138 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 7490138 |
Reference Allele: T | Alternative Allele: G |
Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 304. )
ATTATAGGGACCCAAGTATGTGTTTAGCTTGTTAGGGAATTGTGATTTGCACAGATTATCAGGCATACTTGTTGTCAAATCTGTCTTACTCTCATTTTTT[T/G]
AAGTGCCAGCATACTGTCAAGAATTAATGAATTATAAATTCTTCAAATTTACATATACATCACTTCAAAAGGCTTGTGCATAAGGTGTTGTGACTGAAAT
ATTTCAGTCACAACACCTTATGCACAAGCCTTTTGAAGTGATGTATATGTAAATTTGAAGAATTTATAATTCATTAATTCTTGACAGTATGCTGGCACTT[A/C]
AAAAAATGAGAGTAAGACAGATTTGACAACAAGTATGCCTGATAATCTGTGCAAATCACAATTCCCTAACAAGCTAAACACATACTTGGGTCCCTATAAT
Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 95.30% | 2.80% | 1.95% | 0.00% | NA |
All Indica | 2759 | 99.90% | 0.10% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 86.20% | 8.10% | 5.69% | 0.00% | NA |
Aus | 269 | 98.10% | 0.70% | 1.12% | 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 | 99.50% | 0.40% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 87.70% | 4.80% | 7.43% | 0.00% | NA |
Tropical Japonica | 504 | 92.10% | 6.20% | 1.79% | 0.00% | NA |
Japonica Intermediate | 241 | 69.30% | 22.40% | 8.30% | 0.00% | NA |
VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 95.60% | 2.20% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0607490138 | T -> G | LOC_Os06g13570.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.22; most accessible tissue: Callus, score: 59.779 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0607490138 | 2.23E-06 | 2.23E-06 | mr1181_2 | 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 |