Variant ID: vg1002814950 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 2814950 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 105. )
ACATATCACTTAAATGGTTATGATAACATGTATTATCATGTGATATATCACTCCATAAATATAGAGTAAAATACAGTAGCGGCCCTTAAACTTGCGGGCG[G/A]
ATGTCATCCAGGTCCACTAACTTGCAAATCGTGTAATTAGGCCACTAAACTTGCTAAATGTACCATCGCCGGTCCAAAATGCCGTTTGACCGCAGTCGCG
CGCGACTGCGGTCAAACGGCATTTTGGACCGGCGATGGTACATTTAGCAAGTTTAGTGGCCTAATTACACGATTTGCAAGTTAGTGGACCTGGATGACAT[C/T]
CGCCCGCAAGTTTAAGGGCCGCTACTGTATTTTACTCTATATTTATGGAGTGATATATCACATGATAATACATGTTATCATAACCATTTAAGTGATATGT
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 83.60% | 12.10% | 4.30% | 0.00% | NA |
All Indica | 2759 | 74.30% | 20.70% | 5.04% | 0.00% | NA |
All Japonica | 1512 | 95.80% | 0.10% | 4.03% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 55.00% | 31.10% | 13.95% | 0.00% | NA |
Indica II | 465 | 81.90% | 14.00% | 4.09% | 0.00% | NA |
Indica III | 913 | 77.70% | 21.70% | 0.66% | 0.00% | NA |
Indica Intermediate | 786 | 80.50% | 15.50% | 3.94% | 0.00% | NA |
Temperate Japonica | 767 | 91.90% | 0.10% | 7.95% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 94.40% | 2.20% | 3.33% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1002814950 | G -> A | LOC_Os10g05630.1 | upstream_gene_variant ; 1117.0bp to feature; MODIFIER | silent_mutation | Average:52.589; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
vg1002814950 | G -> A | LOC_Os10g05650.1 | downstream_gene_variant ; 1394.0bp to feature; MODIFIER | silent_mutation | Average:52.589; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
vg1002814950 | G -> A | LOC_Os10g05630-LOC_Os10g05650 | intergenic_region ; MODIFIER | silent_mutation | Average:52.589; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1002814950 | NA | 8.01E-11 | mr1403 | 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 |
vg1002814950 | NA | 7.55E-09 | mr1403 | 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 |
vg1002814950 | NA | 6.26E-06 | mr1547 | 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 |
vg1002814950 | NA | 1.03E-09 | mr1709_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 |