Variant ID: vg0404659256 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 4659256 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 254. )
CACCATCAGTGTCGTACAACTGCTAACACTTTACCCCTGCTGAGGACGTCCTTTGCCTCCAGCCTCCTTCTTCGGCATCAACGTCACCCACCTTCTCCGG[T/C]
GCCGCTCACCCCATCACCTACTGTCCAAGCGTCGCTGCTCCCCAACCTTATTTGCCTTCCTCTTTCTCTCATTCCAAGGTCACTTAAATTCCTAGGTATT
AATACCTAGGAATTTAAGTGACCTTGGAATGAGAGAAAGAGGAAGGCAAATAAGGTTGGGGAGCAGCGACGCTTGGACAGTAGGTGATGGGGTGAGCGGC[A/G]
CCGGAGAAGGTGGGTGACGTTGATGCCGAAGAAGGAGGCTGGAGGCAAAGGACGTCCTCAGCAGGGGTAAAGTGTTAGCAGTTGTACGACACTGATGGTG
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 | 75.70% | 24.10% | 0.13% | 0.00% | NA |
All Indica | 2759 | 93.60% | 6.40% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 40.90% | 58.70% | 0.40% | 0.00% | NA |
Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
Indica I | 595 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
Indica II | 465 | 86.90% | 13.10% | 0.00% | 0.00% | NA |
Indica III | 913 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 90.50% | 9.50% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 12.40% | 87.60% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 77.00% | 21.80% | 1.19% | 0.00% | NA |
Japonica Intermediate | 241 | 56.00% | 44.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 46.90% | 53.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 75.60% | 24.40% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0404659256 | T -> C | LOC_Os04g08570-LOC_Os04g08580 | intergenic_region ; MODIFIER | silent_mutation | Average:58.18; most accessible tissue: Zhenshan97 young leaf, score: 88.259 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0404659256 | NA | 4.54E-10 | mr1023_2 | 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 |
vg0404659256 | 5.57E-07 | 1.09E-15 | mr1178_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 |
vg0404659256 | NA | 5.33E-08 | mr1399_2 | 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 |
vg0404659256 | NA | 7.93E-09 | mr1746_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 |