| Variant ID: vg0508659205 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 8659205 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTGATATGTAGCTCCAGCACTTTTTAATCCAAAAGTCATTACAACCTATTCATATAAGCCGATTGCACCAAGACATCTGAAAGCAGTCTTATGAATATC[C/T]
TCTTCTACCATAAAAATTTGATTATATCCAGCATTGCCATCGATAAAACTTATAATCTTGTGCCCTGAAGCAGCATCTACCAACTGATCGGCAATCGGCA
TGCCGATTGCCGATCAGTTGGTAGATGCTGCTTCAGGGCACAAGATTATAAGTTTTATCGATGGCAATGCTGGATATAATCAAATTTTTATGGTAGAAGA[G/A]
GATATTCATAAGACTGCTTTCAGATGTCTTGGTGCAATCGGCTTATATGAATAGGTTGTAATGACTTTTGGATTAAAAAGTGCTGGAGCTACATATCAAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.60% | 6.90% | 0.93% | 3.49% | NA |
| All Indica | 2759 | 87.60% | 4.90% | 1.56% | 5.94% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 29.00% | 70.60% | 0.37% | 0.00% | NA |
| Indica I | 595 | 98.20% | 0.00% | 0.34% | 1.51% | NA |
| Indica II | 465 | 98.50% | 0.20% | 0.65% | 0.65% | NA |
| Indica III | 913 | 77.50% | 10.40% | 2.41% | 9.64% | NA |
| Indica Intermediate | 786 | 85.00% | 4.80% | 2.04% | 8.14% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0508659205 | C -> T | LOC_Os05g15260.1 | downstream_gene_variant ; 2936.0bp to feature; MODIFIER | silent_mutation | Average:30.184; most accessible tissue: Zhenshan97 young leaf, score: 50.0 | N | N | N | N |
| vg0508659205 | C -> T | LOC_Os05g15270.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.184; most accessible tissue: Zhenshan97 young leaf, score: 50.0 | N | N | N | N |
| vg0508659205 | C -> DEL | N | N | silent_mutation | Average:30.184; most accessible tissue: Zhenshan97 young leaf, score: 50.0 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0508659205 | 1.57E-06 | 1.10E-22 | mr1244 | 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 |
| vg0508659205 | NA | 1.98E-06 | mr1262 | 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 |
| vg0508659205 | NA | 1.67E-06 | mr1286 | 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 |
| vg0508659205 | NA | 1.75E-06 | mr1777 | 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 |