| Variant ID: vg1008319187 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 8319187 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTCCTTCTTGTAGCAAAACACCACCTGTCGAAACAAGATTTCAGCAATACTAAAAGGGGGTGGCTATCAAGCTGGAAAAGTGGATGGGTTAAGAGACAAG[G/T]
GATTTTATACAGGTTCAGGCCTTCTTATTCAAGAAGTAATACCCTACTCCTGTCCGGGGATTGACCCACCGAGTGTATTATTGATCGTATGATCTGGGAG
CTCCCAGATCATACGATCAATAATACACTCGGTGGGTCAATCCCCGGACAGGAGTAGGGTATTACTTCTTGAATAAGAAGGCCTGAACCTGTATAAAATC[C/A]
CTTGTCTCTTAACCCATCCACTTTTCCAGCTTGATAGCCACCCCCTTTTAGTATTGCTGAAATCTTGTTTCGACAGGTGGTGTTTTGCTACAAGAAGGAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.10% | 1.30% | 0.83% | 0.74% | NA |
| All Indica | 2759 | 96.50% | 1.60% | 0.72% | 1.23% | NA |
| All Japonica | 1512 | 98.80% | 0.70% | 0.53% | 0.00% | NA |
| Aus | 269 | 92.20% | 3.30% | 4.09% | 0.37% | NA |
| Indica I | 595 | 98.80% | 0.20% | 1.01% | 0.00% | NA |
| Indica II | 465 | 92.30% | 3.20% | 1.29% | 3.23% | NA |
| Indica III | 913 | 97.40% | 1.40% | 0.11% | 1.10% | NA |
| Indica Intermediate | 786 | 96.20% | 1.80% | 0.89% | 1.15% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 1.00% | 1.39% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.20% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1008319187 | G -> T | LOC_Os10g16670.1 | upstream_gene_variant ; 2574.0bp to feature; MODIFIER | silent_mutation | Average:29.407; most accessible tissue: Minghui63 flag leaf, score: 50.629 | N | N | N | N |
| vg1008319187 | G -> T | LOC_Os10g16680.1 | upstream_gene_variant ; 1277.0bp to feature; MODIFIER | silent_mutation | Average:29.407; most accessible tissue: Minghui63 flag leaf, score: 50.629 | N | N | N | N |
| vg1008319187 | G -> T | LOC_Os10g16690.1 | upstream_gene_variant ; 1475.0bp to feature; MODIFIER | silent_mutation | Average:29.407; most accessible tissue: Minghui63 flag leaf, score: 50.629 | N | N | N | N |
| vg1008319187 | G -> T | LOC_Os10g16700.1 | downstream_gene_variant ; 4832.0bp to feature; MODIFIER | silent_mutation | Average:29.407; most accessible tissue: Minghui63 flag leaf, score: 50.629 | N | N | N | N |
| vg1008319187 | G -> T | LOC_Os10g16680-LOC_Os10g16690 | intergenic_region ; MODIFIER | silent_mutation | Average:29.407; most accessible tissue: Minghui63 flag leaf, score: 50.629 | N | N | N | N |
| vg1008319187 | G -> DEL | N | N | silent_mutation | Average:29.407; most accessible tissue: Minghui63 flag leaf, score: 50.629 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1008319187 | NA | 2.46E-06 | Awn_length | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1008319187 | 1.49E-08 | NA | mr1877 | 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 |
| vg1008319187 | 6.50E-06 | NA | mr1877 | 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 |