| Variant ID: vg0907789558 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 7789558 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.32, others allele: 0.00, population size: 72. )
TAAAACCGACATCTATGAAGCTTTTTTCACCTTTTTACAATATAAAAGTAAGAACTGGTACATATAATCACTCATTGGCACTGGTTTATAACAAAACTGA[C/T]
ATAATTAATCCCCCAAATCATAGGTGTTGATTCTTTTTATAAACCGGTACCTGTAGACATCACACAGGTGCTGGTTCTTATAATAAACTGGCACATACAA
TTGTATGTGCCAGTTTATTATAAGAACCAGCACCTGTGTGATGTCTACAGGTACCGGTTTATAAAAAGAATCAACACCTATGATTTGGGGGATTAATTAT[G/A]
TCAGTTTTGTTATAAACCAGTGCCAATGAGTGATTATATGTACCAGTTCTTACTTTTATATTGTAAAAAGGTGAAAAAAGCTTCATAGATGTCGGTTTTA
| 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 | 86.50% | 13.10% | 0.02% | 0.40% | NA |
| All Indica | 2759 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 65.30% | 33.40% | 0.07% | 1.26% | NA |
| Aus | 269 | 78.80% | 21.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 38.60% | 61.30% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 95.80% | 0.40% | 0.20% | 3.57% | NA |
| Japonica Intermediate | 241 | 86.30% | 13.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 14.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0907789558 | C -> DEL | N | N | silent_mutation | Average:63.867; most accessible tissue: Callus, score: 80.708 | N | N | N | N |
| vg0907789558 | C -> T | LOC_Os09g13460-LOC_Os09g13470 | intergenic_region ; MODIFIER | silent_mutation | Average:63.867; most accessible tissue: Callus, score: 80.708 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0907789558 | 4.09E-06 | 3.63E-20 | mr1010_2 | 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 |
| vg0907789558 | 2.37E-06 | 1.51E-12 | mr1010_2 | 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 |
| vg0907789558 | NA | 1.93E-07 | mr1013_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 |
| vg0907789558 | NA | 3.20E-06 | mr1330_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 |