| Variant ID: vg0138783200 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 38783200 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGGTGATGAGCGCGGGTTCCTATTTCTCGTTTAGTGTCGCCCCGATCTTGATGGTCTTGTCGGGGTTGGCACTGGAGAGTGGAACGATCTTGATGGCGCC[G/A]
TCCGGTTTCGGCGTCTTGTTTGTCTTGCTCACTTTCTTGGGTGGCTCAGTCGTGGTGGATGGGCTGGGCGTTTGCTCGACCATGTCAAGGCTCCGCTTGT
ACAAGCGGAGCCTTGACATGGTCGAGCAAACGCCCAGCCCATCCACCACGACTGAGCCACCCAAGAAAGTGAGCAAGACAAACAAGACGCCGAAACCGGA[C/T]
GGCGCCATCAAGATCGTTCCACTCTCCAGTGCCAACCCCGACAAGACCATCAAGATCGGGGCGACACTAAACGAGAAATAGGAACCCGCGCTCATCACCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.30% | 31.80% | 3.62% | 7.30% | NA |
| All Indica | 2759 | 35.80% | 46.80% | 5.51% | 11.96% | NA |
| All Japonica | 1512 | 92.90% | 6.70% | 0.13% | 0.26% | NA |
| Aus | 269 | 66.90% | 27.10% | 3.35% | 2.60% | NA |
| Indica I | 595 | 54.60% | 33.10% | 5.55% | 6.72% | NA |
| Indica II | 465 | 6.00% | 64.90% | 9.46% | 19.57% | NA |
| Indica III | 913 | 44.00% | 42.60% | 3.40% | 9.97% | NA |
| Indica Intermediate | 786 | 29.50% | 51.10% | 5.60% | 13.74% | NA |
| Temperate Japonica | 767 | 97.30% | 2.20% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 85.70% | 14.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.80% | 5.40% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 86.50% | 11.50% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 58.90% | 30.00% | 6.67% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0138783200 | G -> A | LOC_Os01g66780.1 | downstream_gene_variant ; 4135.0bp to feature; MODIFIER | silent_mutation | Average:29.056; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0138783200 | G -> A | LOC_Os01g66800.1 | downstream_gene_variant ; 4163.0bp to feature; MODIFIER | silent_mutation | Average:29.056; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0138783200 | G -> A | LOC_Os01g66790.1 | intron_variant ; MODIFIER | silent_mutation | Average:29.056; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0138783200 | G -> DEL | N | N | silent_mutation | Average:29.056; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0138783200 | 6.48E-06 | 6.47E-06 | mr1433_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 |
| vg0138783200 | 1.03E-06 | 1.03E-06 | mr1433_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 |
| vg0138783200 | NA | 3.94E-06 | mr1751_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 |