Variant ID: vg0231359843 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 31359843 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCCGACCGGACGAGACGCACTGTCTCATCCGTGTCGTTTGAGAAGCACTCACTTAGTCGTTTTTAGAAAAGAGTTCAAATAAAATCAATTGCAAAAACAA[T/C]
AGCCTTTCTTTGAAGCCTGCATTAAACACTTATTTCCCATAGCTTGCTGAGTACTCCCGTACTCACCCTTGCTCTATATAAATAATCCCCCCCAGTTGCT
AGCAACTGGGGGGGATTATTTATATAGAGCAAGGGTGAGTACGGGAGTACTCAGCAAGCTATGGGAAATAAGTGTTTAATGCAGGCTTCAAAGAAAGGCT[A/G]
TTGTTTTTGCAATTGATTTTATTTGAACTCTTTTCTAAAAACGACTAAGTGAGTGCTTCTCAAACGACACGGATGAGACAGTGCGTCTCGTCCGGTCGGA
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 | 49.70% | 0.00% | 24.33% | 25.98% | NA |
All Indica | 2759 | 23.70% | 0.00% | 34.94% | 41.36% | NA |
All Japonica | 1512 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
Aus | 269 | 10.80% | 0.00% | 61.71% | 27.51% | NA |
Indica I | 595 | 6.60% | 0.00% | 25.71% | 67.73% | NA |
Indica II | 465 | 37.60% | 0.20% | 30.75% | 31.40% | NA |
Indica III | 913 | 24.00% | 0.00% | 42.28% | 33.73% | NA |
Indica Intermediate | 786 | 28.00% | 0.00% | 35.88% | 36.13% | NA |
Temperate Japonica | 767 | 99.50% | 0.00% | 0.13% | 0.39% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
VI/Aromatic | 96 | 96.90% | 0.00% | 3.12% | 0.00% | NA |
Intermediate | 90 | 73.30% | 0.00% | 16.67% | 10.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0231359843 | T -> DEL | N | N | silent_mutation | Average:8.383; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |
vg0231359843 | T -> C | LOC_Os02g51230-LOC_Os02g51240 | intergenic_region ; MODIFIER | silent_mutation | Average:8.383; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0231359843 | 4.27E-07 | 1.19E-07 | mr1011 | 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 |