| Variant ID: vg1208116243 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8116243 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.91, G: 0.09, others allele: 0.00, population size: 77. )
CAGCCAAGCCTCAGCATTGCCGGCGTCAAATCTAGTCGCAGGAGCAGGGGACATGATGAACGGTCCGTTCGCTCGCCTCCCGAGCGATATAGGGAGCGCC[A/G]
AGTCGAACGACCACAGTCCCCACATCGAAGATGCCCCATCGATCTTCGCGACACCATCAACCAGCGCCGCGCACAAGAGGCCATCATTCACCGGATCGCT
AGCGATCCGGTGAATGATGGCCTCTTGTGCGCGGCGCTGGTTGATGGTGTCGCGAAGATCGATGGGGCATCTTCGATGTGGGGACTGTGGTCGTTCGACT[T/C]
GGCGCTCCCTATATCGCTCGGGAGGCGAGCGAACGGACCGTTCATCATGTCCCCTGCTCCTGCGACTAGATTTGACGCCGGCAATGCTGAGGCTTGGCTG
| 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 | 32.50% | 19.30% | 0.61% | 47.57% | NA |
| All Indica | 2759 | 42.00% | 6.00% | 0.80% | 51.18% | NA |
| All Japonica | 1512 | 4.30% | 43.30% | 0.40% | 51.98% | NA |
| Aus | 269 | 94.40% | 2.60% | 0.00% | 2.97% | NA |
| Indica I | 595 | 52.60% | 11.40% | 0.67% | 35.29% | NA |
| Indica II | 465 | 54.20% | 6.00% | 1.08% | 38.71% | NA |
| Indica III | 913 | 30.80% | 1.50% | 0.55% | 67.14% | NA |
| Indica Intermediate | 786 | 39.80% | 7.10% | 1.02% | 52.04% | NA |
| Temperate Japonica | 767 | 6.30% | 68.40% | 0.26% | 25.03% | NA |
| Tropical Japonica | 504 | 1.80% | 11.70% | 0.60% | 85.91% | NA |
| Japonica Intermediate | 241 | 3.30% | 29.50% | 0.41% | 66.80% | NA |
| VI/Aromatic | 96 | 38.50% | 54.20% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 24.40% | 35.60% | 1.11% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208116243 | A -> DEL | N | N | silent_mutation | Average:15.142; most accessible tissue: Callus, score: 48.04 | N | N | N | N |
| vg1208116243 | A -> G | LOC_Os12g14260.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.142; most accessible tissue: Callus, score: 48.04 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208116243 | NA | 1.14E-09 | mr1198 | 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 |
| vg1208116243 | NA | 2.93E-06 | mr1583 | 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 |
| vg1208116243 | 4.80E-06 | 4.80E-06 | mr1601 | 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 |
| vg1208116243 | 4.14E-06 | 4.13E-06 | mr1448_2 | 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 |
| vg1208116243 | NA | 1.47E-08 | mr1645_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 |