Variant ID: vg0334809884 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 34809884 |
Reference Allele: C | Alternative Allele: T |
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: 268. )
CCATCCACAATTTCTTTCTGTCAGTTTCCTTGACTGTCAAAATACTACTCCCTCTGTCCCTAAATATTTGACGCCGTTGACTTTTTTAAACATGTTGGAC[C/T]
GTTCGTCTTATTCAAAAAATTTAAGTAATTATTAATTCTTTTCCTATCATTTGATTCATTGTTAAATATACTACTACTACTCAAGTTTTTTAATAATATT
AATATTATTAAAAAACTTGAGTAGTAGTAGTATATTTAACAATGAATCAAATGATAGGAAAAGAATTAATAATTACTTAAATTTTTTGAATAAGACGAAC[G/A]
GTCCAACATGTTTAAAAAAGTCAACGGCGTCAAATATTTAGGGACAGAGGGAGTAGTATTTTGACAGTCAAGGAAACTGACAGAAAGAAATTGTGGATGG
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 | 90.70% | 9.30% | 0.02% | 0.00% | NA |
All Indica | 2759 | 84.50% | 15.50% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
Indica II | 465 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
Indica III | 913 | 68.80% | 31.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 85.80% | 14.10% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 93.30% | 6.70% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0334809884 | C -> T | LOC_Os03g61310.1 | upstream_gene_variant ; 193.0bp to feature; MODIFIER | silent_mutation | Average:45.451; most accessible tissue: Zhenshan97 root, score: 66.982 | N | N | N | N |
vg0334809884 | C -> T | LOC_Os03g61290.1 | downstream_gene_variant ; 1978.0bp to feature; MODIFIER | silent_mutation | Average:45.451; most accessible tissue: Zhenshan97 root, score: 66.982 | N | N | N | N |
vg0334809884 | C -> T | LOC_Os03g61319.1 | downstream_gene_variant ; 4253.0bp to feature; MODIFIER | silent_mutation | Average:45.451; most accessible tissue: Zhenshan97 root, score: 66.982 | N | N | N | N |
vg0334809884 | C -> T | LOC_Os03g61290-LOC_Os03g61310 | intergenic_region ; MODIFIER | silent_mutation | Average:45.451; most accessible tissue: Zhenshan97 root, score: 66.982 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0334809884 | 4.44E-06 | 3.55E-07 | mr1094 | 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 |
vg0334809884 | NA | 7.15E-06 | mr1305 | 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 |
vg0334809884 | 7.21E-06 | 7.21E-06 | mr1355 | 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 |
vg0334809884 | NA | 7.40E-06 | mr1765 | 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 |
vg0334809884 | NA | 5.15E-06 | mr1096_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 |