Variant ID: vg0807648774 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 7648774 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGAGTTCATCTGTGACGGGCTCTAGTTTAGGCCCGATTGAGATCAGTAGTCATCTGTAACGGGCTCTAGTTTAGGCCCGATTGAGGTCAGTAGTCATCTG[T/C]
GATGGGCTCTAGTTTAGGCCCGATTGAGGTCAGTAGTCATCTGTGACGGGCTATAGTTTAGGCCCGATTGAGATGTGTATCATCTGTGATGGGCTCTAGT
ACTAGAGCCCATCACAGATGATACACATCTCAATCGGGCCTAAACTATAGCCCGTCACAGATGACTACTGACCTCAATCGGGCCTAAACTAGAGCCCATC[A/G]
CAGATGACTACTGACCTCAATCGGGCCTAAACTAGAGCCCGTTACAGATGACTACTGATCTCAATCGGGCCTAAACTAGAGCCCGTCACAGATGAACTCA
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 96.00% | 1.90% | 2.01% | 0.06% | NA |
All Indica | 2759 | 93.40% | 3.20% | 3.37% | 0.11% | NA |
All Japonica | 1512 | 99.80% | 0.10% | 0.13% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 96.00% | 1.70% | 2.35% | 0.00% | NA |
Indica II | 465 | 93.80% | 2.80% | 3.23% | 0.22% | NA |
Indica III | 913 | 92.70% | 3.50% | 3.72% | 0.11% | NA |
Indica Intermediate | 786 | 92.00% | 4.10% | 3.82% | 0.13% | NA |
Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 99.60% | 0.20% | 0.20% | 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 | 97.80% | 2.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0807648774 | T -> C | LOC_Os08g12890.1 | upstream_gene_variant ; 3809.0bp to feature; MODIFIER | silent_mutation | Average:45.807; most accessible tissue: Minghui63 flag leaf, score: 73.334 | N | N | N | N |
vg0807648774 | T -> C | LOC_Os08g12880.1 | downstream_gene_variant ; 2472.0bp to feature; MODIFIER | silent_mutation | Average:45.807; most accessible tissue: Minghui63 flag leaf, score: 73.334 | N | N | N | N |
vg0807648774 | T -> C | LOC_Os08g12880-LOC_Os08g12890 | intergenic_region ; MODIFIER | silent_mutation | Average:45.807; most accessible tissue: Minghui63 flag leaf, score: 73.334 | N | N | N | N |
vg0807648774 | T -> DEL | N | N | silent_mutation | Average:45.807; most accessible tissue: Minghui63 flag leaf, score: 73.334 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0807648774 | 1.01E-06 | NA | mr1350_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 |
vg0807648774 | 3.09E-06 | NA | mr1350_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 |