| Variant ID: vg0814220368 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14220368 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGGTTTGCCAGTACTCACCTAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAGTGCACACCGGTGAATTTATCCGGC[C/T]
TCAATGTATCGGCAAAACCAGCCATAGTAAAATCACAGTGCCTATAATAAGGTTTTTGGATTGTTGAGATTAAAGGCATATAATGATTTAATATATTCCA
TGGAATATATTAAATCATTATATGCCTTTAATCTCAACAATCCAAAAACCTTATTATAGGCACTGTGATTTTACTATGGCTGGTTTTGCCGATACATTGA[G/A]
GCCGGATAAATTCACCGGTGTGCACTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTAGGTGAGTACTGGCAAACCT
| 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 | 53.20% | 19.50% | 14.56% | 12.70% | NA |
| All Indica | 2759 | 81.10% | 1.20% | 16.96% | 0.69% | NA |
| All Japonica | 1512 | 11.90% | 56.20% | 4.76% | 27.18% | NA |
| Aus | 269 | 17.10% | 2.20% | 43.12% | 37.55% | NA |
| Indica I | 595 | 74.10% | 0.70% | 25.21% | 0.00% | NA |
| Indica II | 465 | 77.20% | 1.70% | 20.86% | 0.22% | NA |
| Indica III | 913 | 89.50% | 1.10% | 8.76% | 0.66% | NA |
| Indica Intermediate | 786 | 79.00% | 1.50% | 17.94% | 1.53% | NA |
| Temperate Japonica | 767 | 11.00% | 84.60% | 2.48% | 1.96% | NA |
| Tropical Japonica | 504 | 13.90% | 24.00% | 6.35% | 55.75% | NA |
| Japonica Intermediate | 241 | 10.80% | 32.80% | 8.71% | 47.72% | NA |
| VI/Aromatic | 96 | 11.50% | 9.40% | 26.04% | 53.12% | NA |
| Intermediate | 90 | 44.40% | 27.80% | 7.78% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814220368 | C -> T | LOC_Os08g23480.1 | upstream_gene_variant ; 34.0bp to feature; MODIFIER | silent_mutation | Average:33.245; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 | N | N | N | N |
| vg0814220368 | C -> T | LOC_Os08g23490.1 | upstream_gene_variant ; 2457.0bp to feature; MODIFIER | silent_mutation | Average:33.245; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 | N | N | N | N |
| vg0814220368 | C -> T | LOC_Os08g23480-LOC_Os08g23490 | intergenic_region ; MODIFIER | silent_mutation | Average:33.245; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 | N | N | N | N |
| vg0814220368 | C -> DEL | N | N | silent_mutation | Average:33.245; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0814220368 | 2.34E-07 | NA | mr1141 | 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 |
| vg0814220368 | NA | 4.46E-07 | mr1321 | 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 |
| vg0814220368 | NA | 1.48E-09 | mr1649_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 |
| vg0814220368 | NA | 3.54E-06 | mr1788_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 |