| Variant ID: vg1216237013 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16237013 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 89. )
TAGGTGATGTGGATCCAAGTTAAGCTATAGGTACTAAGGCTATTGGAGACATACGACCAGTCGAGACGCAGGATGACCAAGAAGATAGGGATCAACCTTC[A/G]
TCATCGACATCCAATAGCCCTACATCGAGTCGAGATACAGTTGACCCGGAAGTTTCGGGACCAGATGATCGCAACCTCCGGACCTCTCTAGGCCAGGAAG
CTTCCTGGCCTAGAGAGGTCCGGAGGTTGCGATCATCTGGTCCCGAAACTTCCGGGTCAACTGTATCTCGACTCGATGTAGGGCTATTGGATGTCGATGA[T/C]
GAAGGTTGATCCCTATCTTCTTGGTCATCCTGCGTCTCGACTGGTCGTATGTCTCCAATAGCCTTAGTACCTATAGCTTAACTTGGATCCACATCACCTA
| 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 | 43.90% | 5.50% | 6.56% | 44.05% | NA |
| All Indica | 2759 | 31.20% | 3.20% | 8.95% | 56.69% | NA |
| All Japonica | 1512 | 61.80% | 5.20% | 1.92% | 31.02% | NA |
| Aus | 269 | 69.90% | 12.60% | 9.29% | 8.18% | NA |
| Indica I | 595 | 38.00% | 0.70% | 3.36% | 57.98% | NA |
| Indica II | 465 | 42.40% | 2.40% | 12.69% | 42.58% | NA |
| Indica III | 913 | 15.10% | 4.70% | 11.28% | 68.89% | NA |
| Indica Intermediate | 786 | 38.20% | 3.70% | 8.27% | 49.87% | NA |
| Temperate Japonica | 767 | 89.40% | 6.50% | 0.13% | 3.91% | NA |
| Tropical Japonica | 504 | 16.50% | 1.20% | 5.36% | 76.98% | NA |
| Japonica Intermediate | 241 | 68.90% | 9.50% | 0.41% | 21.16% | NA |
| VI/Aromatic | 96 | 35.40% | 54.20% | 2.08% | 8.33% | NA |
| Intermediate | 90 | 61.10% | 10.00% | 7.78% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216237013 | A -> DEL | N | N | silent_mutation | Average:10.09; most accessible tissue: Callus, score: 42.763 | N | N | N | N |
| vg1216237013 | A -> G | LOC_Os12g27590.1 | upstream_gene_variant ; 2801.0bp to feature; MODIFIER | silent_mutation | Average:10.09; most accessible tissue: Callus, score: 42.763 | N | N | N | N |
| vg1216237013 | A -> G | LOC_Os12g27580.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.09; most accessible tissue: Callus, score: 42.763 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216237013 | 1.86E-06 | 1.75E-06 | mr1745 | 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 |
| vg1216237013 | 2.07E-06 | NA | mr1778 | 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 |
| vg1216237013 | NA | 1.96E-08 | mr1057_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 |
| vg1216237013 | 3.94E-07 | NA | mr1489_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 |
| vg1216237013 | 5.80E-07 | NA | mr1778_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 |