Variant ID: vg0235926582 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 35926582 |
Reference Allele: A | Alternative Allele: T |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 123. )
CATGCAATTAGCTAGCACCTCGTTTCCACTAAATTATTATTTTTTAAATCCTTGACACTCAAGATGTTTAGGTTGTGTTTAGTTCACACTGAAGTTTGGA[A/T]
GTTTGGTTGAAATTGGTACGACGTGATAGAAAAAGTTGTGTGTATGAAAGGTTTGATGTAATGAAAAGTTGGAAGTTTGGAAAAAAAACTTTGGAACTAA
TTAGTTCCAAAGTTTTTTTTCCAAACTTCCAACTTTTCATTACATCAAACCTTTCATACACACAACTTTTTCTATCACGTCGTACCAATTTCAACCAAAC[T/A]
TCCAAACTTCAGTGTGAACTAAACACAACCTAAACATCTTGAGTGTCAAGGATTTAAAAAATAATAATTTAGTGGAAACGAGGTGCTAGCTAATTGCATG
Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 95.70% | 3.60% | 0.66% | 0.00% | NA |
All Indica | 2759 | 93.00% | 5.80% | 1.12% | 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 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
Indica II | 465 | 72.70% | 24.10% | 3.23% | 0.00% | NA |
Indica III | 913 | 98.80% | 1.10% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 93.40% | 5.00% | 1.65% | 0.00% | NA |
Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 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% | 5.60% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0235926582 | A -> T | LOC_Os02g58800.1 | upstream_gene_variant ; 3220.0bp to feature; MODIFIER | silent_mutation | Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 | N | N | N | N |
vg0235926582 | A -> T | LOC_Os02g58790.1 | intron_variant ; MODIFIER | silent_mutation | Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 | N | N | N | N |
vg0235926582 | A -> T | LOC_Os02g58790.2 | intron_variant ; MODIFIER | silent_mutation | Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 | N | N | N | N |
vg0235926582 | A -> T | LOC_Os02g58790.3 | intron_variant ; MODIFIER | silent_mutation | Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 | N | N | N | N |
vg0235926582 | A -> T | LOC_Os02g58790.4 | intron_variant ; MODIFIER | silent_mutation | Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 | N | N | N | N |
vg0235926582 | A -> T | LOC_Os02g58790.5 | intron_variant ; MODIFIER | silent_mutation | Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0235926582 | NA | 1.33E-06 | mr1002_2 | 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 |
vg0235926582 | NA | 4.70E-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 |