Variant ID: vg1124320519 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 24320519 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )
AAAACAAGAATTAATGTTGAATTAGAGAATATTGATTCGCGTGTATCCGTAACATCGGACATGTGGACCTCAAGTCGAAACTTAGGATACATGCTTGTCA[T/C]
AGCACATTATGTTAATGAAAAATTCAAAATGAAAAAGAAAATTATAAGTTTGAAGTATGTGAAGTATCCACACACTAGCTTTGCAATTAGAGAAGCCATG
CATGGCTTCTCTAATTGCAAAGCTAGTGTGTGGATACTTCACATACTTCAAACTTATAATTTTCTTTTTCATTTTGAATTTTTCATTAACATAATGTGCT[A/G]
TGACAAGCATGTATCCTAAGTTTCGACTTGAGGTCCACATGTCCGATGTTACGGATACACGCGAATCAATATTCTCTAATTCAACATTAATTCTTGTTTT
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 | 93.80% | 6.20% | 0.04% | 0.00% | NA |
All Indica | 2759 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 81.20% | 18.70% | 0.13% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 65.70% | 34.00% | 0.26% | 0.00% | NA |
Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 92.50% | 7.50% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 96.70% | 3.30% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1124320519 | T -> C | LOC_Os11g40700.1 | downstream_gene_variant ; 3363.0bp to feature; MODIFIER | silent_mutation | Average:48.207; most accessible tissue: Callus, score: 85.441 | N | N | N | N |
vg1124320519 | T -> C | LOC_Os11g40690-LOC_Os11g40700 | intergenic_region ; MODIFIER | silent_mutation | Average:48.207; most accessible tissue: Callus, score: 85.441 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1124320519 | NA | 2.43E-07 | mr1617 | 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 |
vg1124320519 | 4.44E-06 | 4.44E-06 | mr1728 | 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 |
vg1124320519 | NA | 9.67E-08 | mr1010_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 |
vg1124320519 | NA | 3.45E-07 | mr1748_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 |