| Variant ID: vg0500436456 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 436456 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 281. )
TGTGTGTGGAGCGGCAACTAGTGGTTATTGGTGGTCTAAGGAGTTTGCCGTTGATACAATCCCCAACCTTGTTTGTTGCATTTTTTTTCTCTGAGTACTA[T/A]
CAATATATTTGTCCATCAATAATCATAAAGAAATAGCTAGTTTTAAAGTAGTAAAAAAATTGAGATAAAGGTGGAGTACTCGAGTAGGGATGAAAACGCT
AGCGTTTTCATCCCTACTCGAGTACTCCACCTTTATCTCAATTTTTTTACTACTTTAAAACTAGCTATTTCTTTATGATTATTGATGGACAAATATATTG[A/T]
TAGTACTCAGAGAAAAAAAATGCAACAAACAAGGTTGGGGATTGTATCAACGGCAAACTCCTTAGACCACCAATAACCACTAGTTGCCGCTCCACACACA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.80% | 5.90% | 1.31% | 1.02% | NA |
| All Indica | 2759 | 89.40% | 6.70% | 2.17% | 1.70% | NA |
| All Japonica | 1512 | 96.80% | 3.10% | 0.07% | 0.07% | NA |
| Aus | 269 | 85.90% | 14.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 83.40% | 13.80% | 2.18% | 0.67% | NA |
| Indica II | 465 | 97.00% | 0.00% | 1.72% | 1.29% | NA |
| Indica III | 913 | 92.80% | 1.80% | 2.41% | 3.07% | NA |
| Indica Intermediate | 786 | 85.50% | 11.20% | 2.16% | 1.15% | NA |
| Temperate Japonica | 767 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0500436456 | T -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0500436456 | T -> A | LOC_Os05g01700.1 | upstream_gene_variant ; 4720.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0500436456 | T -> A | LOC_Os05g01710.1 | upstream_gene_variant ; 557.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0500436456 | T -> A | LOC_Os05g01710.3 | upstream_gene_variant ; 554.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0500436456 | T -> A | LOC_Os05g01710.2 | upstream_gene_variant ; 557.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0500436456 | T -> A | LOC_Os05g01700-LOC_Os05g01710 | intergenic_region ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0500436456 | NA | 1.69E-06 | mr1066 | 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 |
| vg0500436456 | 2.45E-06 | 2.14E-08 | mr1126 | 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 |
| vg0500436456 | NA | 5.88E-06 | mr1457 | 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 |
| vg0500436456 | NA | 1.04E-07 | mr1458 | 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 |
| vg0500436456 | NA | 8.70E-06 | mr1513 | 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 |
| vg0500436456 | NA | 2.07E-06 | mr1525 | 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 |
| vg0500436456 | 1.99E-06 | 2.00E-06 | mr1673 | 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 |
| vg0500436456 | NA | 8.93E-06 | mr1974 | 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 |
| vg0500436456 | NA | 3.05E-07 | mr1380_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 |
| vg0500436456 | NA | 2.11E-07 | mr1458_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 |
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