Variant ID: vg1124122024 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 24122024 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.60, C: 0.39, others allele: 0.00, population size: 268. )
CATTTTGGGTATTGTTCTTTTCTTTAGGCATCAATTTATCATACCTTTCCTGTAGAGACTCACAGCCTTTAAGAATATCATCGTGAGCAAGTGTCACGGC[T/C]
TCTTGAAAAATCATATTGGGCACAAAAAAGCTGTCAGGGATCAGGTCAGGCTTTGAAACCAGTAGATATGCACAGTATCGCGACAAGCTATTCGCGATGA
TCATCGCGAATAGCTTGTCGCGATACTGTGCATATCTACTGGTTTCAAAGCCTGACCTGATCCCTGACAGCTTTTTTGTGCCCAATATGATTTTTCAAGA[A/G]
GCCGTGACACTTGCTCACGATGATATTCTTAAAGGCTGTGAGTCTCTACAGGAAAGGTATGATAAATTGATGCCTAAAGAAAAGAACAATACCCAAAATG
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 | 71.40% | 28.60% | 0.00% | 0.00% | NA |
All Indica | 2759 | 72.30% | 27.70% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 69.00% | 31.00% | 0.00% | 0.00% | NA |
Aus | 269 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
Indica I | 595 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
Indica II | 465 | 74.40% | 25.60% | 0.00% | 0.00% | NA |
Indica III | 913 | 56.20% | 43.80% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 72.00% | 28.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 84.00% | 16.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 51.00% | 49.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 59.30% | 40.70% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 31.20% | 68.80% | 0.00% | 0.00% | NA |
Intermediate | 90 | 67.80% | 32.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1124122024 | T -> C | LOC_Os11g40450.1 | synonymous_variant ; p.Glu1872Glu; LOW | synonymous_codon | Average:48.836; most accessible tissue: Callus, score: 78.651 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1124122024 | NA | 5.41E-06 | mr1047 | 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 |
vg1124122024 | NA | 3.24E-06 | mr1063 | 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 |
vg1124122024 | NA | 3.38E-08 | mr1133 | 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 |
vg1124122024 | NA | 9.88E-09 | mr1242 | 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 |
vg1124122024 | NA | 1.74E-06 | mr1133_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 |
vg1124122024 | NA | 9.29E-07 | mr1242_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 |
vg1124122024 | NA | 7.97E-06 | mr1246_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 |