| Variant ID: vg1105880412 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5880412 |
| Reference Allele: C | Alternative Allele: G,T |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, G: 0.31, others allele: 0.00, population size: 227. )
GAATCTTCACCGCAATTTTATCTCCATTTTTATGCTCTCCCTGTTAAGTATCTAGGGTCAGTACTCAAAACATCATAAAAGTGGTGCAGGGTTCTGTTTG[C/G,T]
TTTGTCGTTAGACTTTTACTAGAAGTAAGTTTTATTTGCAACAATAAAAAGTGGTGCATGGTTGATTGCTCACCTCAGTGTTATTTGTGCAAAACATGCA
TGCATGTTTTGCACAAATAACACTGAGGTGAGCAATCAACCATGCACCACTTTTTATTGTTGCAAATAAAACTTACTTCTAGTAAAAGTCTAACGACAAA[G/C,A]
CAAACAGAACCCTGCACCACTTTTATGATGTTTTGAGTACTGACCCTAGATACTTAACAGGGAGAGCATAAAAATGGAGATAAAATTGCGGTGAAGATTC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.40% | 9.40% | 0.15% | 0.00% | T: 0.04% |
| All Indica | 2759 | 92.80% | 7.20% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 92.20% | 7.40% | 0.26% | 0.00% | T: 0.13% |
| Aus | 269 | 56.10% | 43.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.40% | 2.40% | 0.22% | 0.00% | NA |
| Indica III | 913 | 85.40% | 14.50% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 93.00% | 7.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 97.50% | 2.10% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 84.70% | 15.10% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 90.90% | 8.30% | 0.00% | 0.00% | T: 0.83% |
| VI/Aromatic | 96 | 89.60% | 10.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 8.90% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105880412 | C -> T | LOC_Os11g10710.1 | intron_variant ; MODIFIER | silent_mutation | Average:40.518; most accessible tissue: Minghui63 root, score: 57.225 | N | N | N | N |
| vg1105880412 | C -> G | LOC_Os11g10710.1 | intron_variant ; MODIFIER | silent_mutation | Average:40.518; most accessible tissue: Minghui63 root, score: 57.225 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1105880412 | NA | 2.08E-06 | mr1236 | 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 |
| vg1105880412 | 1.05E-06 | 1.21E-11 | mr1248 | 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 |