| Variant ID: vg0617084846 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 17084846 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCACAAGCTGCCGGCATCGTCATAAATCGTCAAAAAGAAGACGAGGAAGTGTGCCAGCTGAAAAAGGCACTTGGAGAAGCCACTCGCATTGTGAACGTAA[A/G]
TCTTCCGGGTGACTGCCTTTAATGACTTTGTTTTCTCTTCAGCAAAACTAAACCGTGAACCATCATGCAGAGAATCCATCTTCGCAATGAGGCCAAGACT
AGTCTTGGCCTCATTGCGAAGATGGATTCTCTGCATGATGGTTCACGGTTTAGTTTTGCTGAAGAGAAAACAAAGTCATTAAAGGCAGTCACCCGGAAGA[T/C]
TTACGTTCACAATGCGAGTGGCTTCTCCAAGTGCCTTTTTCAGCTGGCACACTTCCTCGTCTTCTTTTTGACGATTTATGACGATGCCGGCAGCTTGTGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.10% | 0.90% | 17.16% | 25.81% | NA |
| All Indica | 2759 | 28.60% | 1.40% | 27.76% | 42.23% | NA |
| All Japonica | 1512 | 98.70% | 0.00% | 0.13% | 1.12% | NA |
| Aus | 269 | 82.90% | 1.10% | 8.18% | 7.81% | NA |
| Indica I | 595 | 22.00% | 1.30% | 24.87% | 51.76% | NA |
| Indica II | 465 | 18.30% | 2.60% | 35.48% | 43.66% | NA |
| Indica III | 913 | 35.70% | 0.90% | 27.27% | 36.14% | NA |
| Indica Intermediate | 786 | 31.60% | 1.30% | 25.95% | 41.22% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.00% | 1.69% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.40% | 0.20% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 83.30% | 1.00% | 12.50% | 3.12% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 10.00% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0617084846 | A -> G | LOC_Os06g29750.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:12.598; most accessible tissue: Minghui63 young leaf, score: 19.077 | N | N | N | N |
| vg0617084846 | A -> G | LOC_Os06g29740.1 | downstream_gene_variant ; 4654.0bp to feature; MODIFIER | silent_mutation | Average:12.598; most accessible tissue: Minghui63 young leaf, score: 19.077 | N | N | N | N |
| vg0617084846 | A -> G | LOC_Os06g29760.1 | downstream_gene_variant ; 1274.0bp to feature; MODIFIER | silent_mutation | Average:12.598; most accessible tissue: Minghui63 young leaf, score: 19.077 | N | N | N | N |
| vg0617084846 | A -> DEL | N | N | silent_mutation | Average:12.598; most accessible tissue: Minghui63 young leaf, score: 19.077 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0617084846 | 3.60E-06 | NA | mr1542 | 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 |