| Variant ID: vg0114001977 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14001977 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 300. )
TTGGGTGTACTTTCTCCATGACAAAAGCGAAGCTCAAGATGTCTTCAAGCGCTTCGCAAAGCAAGCTCAAAACCTCTATGATCTCACTATCAAGAAGGTG[C/A]
GAAGCGACAATGGAGGAGAATTCTAGAACACTCAAGTGGAGGAATTTCTTGATGAAGAAGGAATCAAGCACGAGTTCTCCGCCCCCTATGATCCTCCCCA
TGGGGAGGATCATAGGGGGCGGAGAACTCGTGCTTGATTCCTTCTTCATCAAGAAATTCCTCCACTTGAGTGTTCTAGAATTCTCCTCCATTGTCGCTTC[G/T]
CACCTTCTTGATAGTGAGATCATAGAGGTTTTGAGCTTGCTTTGCGAAGCGCTTGAAGACATCTTGAGCTTCGCTTTTGTCATGGAGAAAGTACACCCAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.70% | 1.10% | 4.17% | 0.00% | NA |
| All Indica | 2759 | 94.80% | 0.40% | 4.86% | 0.00% | NA |
| All Japonica | 1512 | 95.50% | 1.00% | 3.51% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 87.90% | 0.50% | 11.60% | 0.00% | NA |
| Indica II | 465 | 97.60% | 0.20% | 2.15% | 0.00% | NA |
| Indica III | 913 | 99.10% | 0.20% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 93.30% | 0.50% | 6.23% | 0.00% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 1.56% | 0.00% | NA |
| Tropical Japonica | 504 | 89.50% | 3.00% | 7.54% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 61.50% | 29.20% | 9.38% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0114001977 | C -> A | LOC_Os01g24860.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:23.765; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 | N | N | N | N |
| vg0114001977 | C -> A | LOC_Os01g24870.1 | upstream_gene_variant ; 3063.0bp to feature; MODIFIER | silent_mutation | Average:23.765; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0114001977 | 3.80E-07 | 1.04E-08 | mr1064 | 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 |
| vg0114001977 | NA | 8.27E-06 | mr1136 | 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 |
| vg0114001977 | NA | 9.16E-08 | mr1679 | 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 |
| vg0114001977 | NA | 4.85E-06 | mr1741 | 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 |