Variant ID: vg0313149395 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 13149395 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATTATTTTTATAAAAAATTATAGTGCACTTACATATCATATCAACTGAATTTACAAATGTAATTTTAGTTATGTAGGACTGTAATTTTATATTTTAAAAT[A/G]
TAATTTTAGTTATATAAGACTGTAATTTTATTTTTTTTAAAAAAATAACAAATACATATTTACTTATACCAAAATTACAGTGCACTTACATGTCATATCA
TGATATGACATGTAAGTGCACTGTAATTTTGGTATAAGTAAATATGTATTTGTTATTTTTTTAAAAAAAATAAAATTACAGTCTTATATAACTAAAATTA[T/C]
ATTTTAAAATATAAAATTACAGTCCTACATAACTAAAATTACATTTGTAAATTCAGTTGATATGATATGTAAGTGCACTATAATTTTTTATAAAAATAAT
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 88.80% | 9.60% | 1.54% | 0.00% | NA |
All Indica | 2759 | 98.20% | 0.10% | 1.70% | 0.00% | NA |
All Japonica | 1512 | 70.20% | 28.40% | 1.32% | 0.00% | NA |
Aus | 269 | 91.80% | 6.30% | 1.86% | 0.00% | NA |
Indica I | 595 | 98.00% | 0.00% | 2.02% | 0.00% | NA |
Indica II | 465 | 96.10% | 0.00% | 3.87% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 97.70% | 0.30% | 2.04% | 0.00% | NA |
Temperate Japonica | 767 | 57.60% | 40.20% | 2.22% | 0.00% | NA |
Tropical Japonica | 504 | 89.90% | 9.90% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 69.30% | 29.90% | 0.83% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 93.30% | 5.60% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0313149395 | A -> G | LOC_Os03g22770.1 | upstream_gene_variant ; 3565.0bp to feature; MODIFIER | silent_mutation | Average:35.538; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 | N | N | N | N |
vg0313149395 | A -> G | LOC_Os03g22770.2 | upstream_gene_variant ; 3565.0bp to feature; MODIFIER | silent_mutation | Average:35.538; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 | N | N | N | N |
vg0313149395 | A -> G | LOC_Os03g22760.1 | downstream_gene_variant ; 287.0bp to feature; MODIFIER | silent_mutation | Average:35.538; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 | N | N | N | N |
vg0313149395 | A -> G | LOC_Os03g22760-LOC_Os03g22770 | intergenic_region ; MODIFIER | silent_mutation | Average:35.538; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0313149395 | NA | 2.81E-06 | mr1530 | 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 |
vg0313149395 | NA | 7.35E-09 | mr1446_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 |
vg0313149395 | 4.78E-06 | NA | mr1530_2 | 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 |