| Variant ID: vg1001996513 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1996513 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 218. )
CCCGATTTAATAATAAGCTAAAAAAATTTCGTCGGAATATATCCATGTGTGGTCTTGTTTTGAATATTTAATTGCAACGAATTTAATGGTGTAATCGGAT[T/C]
ATGATTTGGATAAATAATTTAAGAGAAAAAATAGTTTAAAGTGGTTTTGCACGCATGCATGGCTCTGACGTTATGCTGACGTTAGCGTCCGATTTTTTCA
TGAAAAAATCGGACGCTAACGTCAGCATAACGTCAGAGCCATGCATGCGTGCAAAACCACTTTAAACTATTTTTTCTCTTAAATTATTTATCCAAATCAT[A/G]
ATCCGATTACACCATTAAATTCGTTGCAATTAAATATTCAAAACAAGACCACACATGGATATATTCCGACGAAATTTTTTTAGCTTATTATTAAATCGGG
| 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 | 78.30% | 15.40% | 6.24% | 0.02% | NA |
| All Indica | 2759 | 81.10% | 9.10% | 9.79% | 0.04% | NA |
| All Japonica | 1512 | 70.60% | 28.80% | 0.66% | 0.00% | NA |
| Aus | 269 | 87.70% | 8.60% | 3.72% | 0.00% | NA |
| Indica I | 595 | 66.90% | 21.30% | 11.76% | 0.00% | NA |
| Indica II | 465 | 84.10% | 7.10% | 8.82% | 0.00% | NA |
| Indica III | 913 | 87.10% | 4.30% | 8.65% | 0.00% | NA |
| Indica Intermediate | 786 | 83.10% | 6.60% | 10.18% | 0.13% | NA |
| Temperate Japonica | 767 | 57.50% | 42.10% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 95.20% | 4.20% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 60.60% | 37.80% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 17.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1001996513 | T -> C | LOC_Os10g04270.1 | downstream_gene_variant ; 2551.0bp to feature; MODIFIER | silent_mutation | Average:36.109; most accessible tissue: Minghui63 root, score: 61.65 | N | N | N | N |
| vg1001996513 | T -> C | LOC_Os10g04260-LOC_Os10g04270 | intergenic_region ; MODIFIER | silent_mutation | Average:36.109; most accessible tissue: Minghui63 root, score: 61.65 | N | N | N | N |
| vg1001996513 | T -> DEL | N | N | silent_mutation | Average:36.109; most accessible tissue: Minghui63 root, score: 61.65 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1001996513 | 1.33E-06 | NA | mr1679 | 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 |
| vg1001996513 | 3.13E-06 | 1.20E-09 | mr1691 | 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 |
| vg1001996513 | NA | 1.70E-06 | mr1691 | 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 |
| vg1001996513 | NA | 1.99E-07 | mr1768 | 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 |
| vg1001996513 | NA | 6.52E-06 | mr1768_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 |