Variant ID: vg0715234696 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 15234696 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, C: 0.04, others allele: 0.00, population size: 57. )
GTAAAAAGAAGAAGCCGACGATGACCCCTTCTAGCACCATGGTTCTCGGTTGGCTAAAGCTGAAACATGGTTGGATCTTGGATGAAGCTGAATATCGATG[G/C]
CTCCTTTGCAAAACAAGATGGGGTGGGAATCGGCATGGTCCTTCGAGATTGCCATGGCTCCCCAATTTTTTCAGCATGTCAATTCATCAATTTTTGTAGT
ACTACAAAAATTGATGAATTGACATGCTGAAAAAATTGGGGAGCCATGGCAATCTCGAAGGACCATGCCGATTCCCACCCCATCTTGTTTTGCAAAGGAG[C/G]
CATCGATATTCAGCTTCATCCAAGATCCAACCATGTTTCAGCTTTAGCCAACCGAGAACCATGGTGCTAGAAGGGGTCATCGTCGGCTTCTTCTTTTTAC
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 64.70% | 35.20% | 0.08% | 0.00% | NA |
All Indica | 2759 | 44.00% | 55.80% | 0.14% | 0.00% | NA |
All Japonica | 1512 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Aus | 269 | 75.50% | 24.50% | 0.00% | 0.00% | NA |
Indica I | 595 | 54.10% | 45.50% | 0.34% | 0.00% | NA |
Indica II | 465 | 20.90% | 78.70% | 0.43% | 0.00% | NA |
Indica III | 913 | 43.20% | 56.80% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 51.10% | 48.90% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 88.50% | 11.50% | 0.00% | 0.00% | NA |
Intermediate | 90 | 63.30% | 36.70% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0715234696 | G -> C | LOC_Os07g26480.1 | downstream_gene_variant ; 1413.0bp to feature; MODIFIER | silent_mutation | Average:64.365; most accessible tissue: Minghui63 flag leaf, score: 81.312 | N | N | N | N |
vg0715234696 | G -> C | LOC_Os07g26490.1 | downstream_gene_variant ; 2470.0bp to feature; MODIFIER | silent_mutation | Average:64.365; most accessible tissue: Minghui63 flag leaf, score: 81.312 | N | N | N | N |
vg0715234696 | G -> C | LOC_Os07g26480.2 | downstream_gene_variant ; 1413.0bp to feature; MODIFIER | silent_mutation | Average:64.365; most accessible tissue: Minghui63 flag leaf, score: 81.312 | N | N | N | N |
vg0715234696 | G -> C | LOC_Os07g26490.2 | downstream_gene_variant ; 2470.0bp to feature; MODIFIER | silent_mutation | Average:64.365; most accessible tissue: Minghui63 flag leaf, score: 81.312 | N | N | N | N |
vg0715234696 | G -> C | LOC_Os07g26480-LOC_Os07g26490 | intergenic_region ; MODIFIER | silent_mutation | Average:64.365; most accessible tissue: Minghui63 flag leaf, score: 81.312 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0715234696 | NA | 1.15E-06 | mr1212 | 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 |
vg0715234696 | NA | 1.46E-06 | mr1528 | 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 |