| Variant ID: vg0515012929 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 15012929 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 241. )
ATACTAATTGATTTCTAGCAGGATTAATTGATCTCTATGTTTGGTAATGTGCAATCAGATATATGTGCAATTGCATAAATTTTCACATGGACTAAACTCT[T/C]
ATTCTTTTTTCTGTTAATCAGGGAACTCTAGTTTGCTCTCCACATGCCATGTCTGAGGTAATACTACATCTAAGTCCACCTCAAAAGGAAGCTATCGAGG
CCTCGATAGCTTCCTTTTGAGGTGGACTTAGATGTAGTATTACCTCAGACATGGCATGTGGAGAGCAAACTAGAGTTCCCTGATTAACAGAAAAAAGAAT[A/G]
AGAGTTTAGTCCATGTGAAAATTTATGCAATTGCACATATATCTGATTGCACATTACCAAACATAGAGATCAATTAATCCTGCTAGAAATCAATTAGTAT
| 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 | 92.30% | 4.00% | 1.40% | 2.35% | NA |
| All Indica | 2759 | 98.00% | 0.80% | 1.23% | 0.00% | NA |
| All Japonica | 1512 | 80.30% | 10.70% | 1.65% | 7.34% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 96.50% | 0.00% | 3.53% | 0.00% | NA |
| Indica II | 465 | 97.60% | 1.70% | 0.65% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.10% | 1.80% | 1.15% | 0.00% | NA |
| Temperate Japonica | 767 | 96.70% | 0.90% | 0.52% | 1.83% | NA |
| Tropical Japonica | 504 | 54.20% | 27.60% | 3.77% | 14.48% | NA |
| Japonica Intermediate | 241 | 82.60% | 6.60% | 0.83% | 9.96% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 3.30% | 5.56% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0515012929 | T -> DEL | N | N | silent_mutation | Average:41.591; most accessible tissue: Zhenshan97 flower, score: 55.587 | N | N | N | N |
| vg0515012929 | T -> C | LOC_Os05g25800.1 | upstream_gene_variant ; 3541.0bp to feature; MODIFIER | silent_mutation | Average:41.591; most accessible tissue: Zhenshan97 flower, score: 55.587 | N | N | N | N |
| vg0515012929 | T -> C | LOC_Os05g25784-LOC_Os05g25800 | intergenic_region ; MODIFIER | silent_mutation | Average:41.591; most accessible tissue: Zhenshan97 flower, score: 55.587 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0515012929 | NA | 2.35E-06 | mr1583 | Jap_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 |
| vg0515012929 | 5.24E-07 | 5.24E-07 | mr1929 | Jap_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 |
| vg0515012929 | NA | 2.15E-06 | mr1422_2 | Jap_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 |
| vg0515012929 | NA | 3.22E-06 | mr1583_2 | Jap_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 |
| vg0515012929 | 5.50E-06 | 6.54E-10 | mr1850_2 | Jap_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 |