| Variant ID: vg1120444961 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20444961 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 54. )
CTCCTGTGCTTCCTAAATCTAAGTTCCTATGGCCTATGGGCTCCTATATCCATAGCATACATATATGGGGTTGGGCCCCTTGACTTCGAGGGCCTAGTGC[G/A]
ATGGCACAGCTCGACCCCCCTCAGGGTCGGACCTGCTCATTTCAGTGAAAACATAGTATATGTAATATACATGGATTATTATAAAATCAAACAAATTAAA
TTTAATTTGTTTGATTTTATAATAATCCATGTATATTACATATACTATGTTTTCACTGAAATGAGCAGGTCCGACCCTGAGGGGGGTCGAGCTGTGCCAT[C/T]
GCACTAGGCCCTCGAAGTCAAGGGGCCCAACCCCATATATGTATGCTATGGATATAGGAGCCCATAGGCCATAGGAACTTAGATTTAGGAAGCACAGGAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.80% | 18.50% | 5.54% | 22.18% | NA |
| All Indica | 2759 | 31.90% | 30.40% | 7.79% | 29.87% | NA |
| All Japonica | 1512 | 91.60% | 1.10% | 2.05% | 5.22% | NA |
| Aus | 269 | 51.70% | 1.50% | 2.97% | 43.87% | NA |
| Indica I | 595 | 9.20% | 24.70% | 18.32% | 47.73% | NA |
| Indica II | 465 | 37.40% | 36.80% | 5.81% | 20.00% | NA |
| Indica III | 913 | 37.20% | 30.80% | 1.42% | 30.56% | NA |
| Indica Intermediate | 786 | 39.60% | 30.70% | 8.40% | 21.37% | NA |
| Temperate Japonica | 767 | 94.40% | 0.90% | 0.78% | 3.91% | NA |
| Tropical Japonica | 504 | 87.50% | 1.80% | 1.79% | 8.93% | NA |
| Japonica Intermediate | 241 | 91.30% | 0.40% | 6.64% | 1.66% | NA |
| VI/Aromatic | 96 | 77.10% | 1.00% | 1.04% | 20.83% | NA |
| Intermediate | 90 | 71.10% | 13.30% | 7.78% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120444961 | G -> A | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 163.0bp to feature; MODIFIER | silent_mutation | Average:38.552; most accessible tissue: Callus, score: 74.376 | N | N | N | N |
| vg1120444961 | G -> DEL | N | N | silent_mutation | Average:38.552; most accessible tissue: Callus, score: 74.376 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1120444961 | NA | 9.57E-06 | mr1531 | Ind_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 |
| vg1120444961 | NA | 3.19E-08 | mr1728 | 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 |