| Variant ID: vg1216131209 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16131209 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACATCCGGCACTGGAATCTCCATGGCTGCCTCCGGCGGTGCAATCTCCATGGTTGCCTCCGGCATTGCAATCTCCGGTGGCACTTCCGGCACTGGATTTT[C/T]
CTTTTGCATCTCGGGTTCCTCCGCCTTATCAGTCACCTTCCTCTTAGGAGGTCTCGGAGGTTTTCCCAACCCCGGTTTAGGCACCACAGGTTTTTGCGTG
CACGCAAAAACCTGTGGTGCCTAAACCGGGGTTGGGAAAACCTCCGAGACCTCCTAAGAGGAAGGTGACTGATAAGGCGGAGGAACCCGAGATGCAAAAG[G/A]
AAAATCCAGTGCCGGAAGTGCCACCGGAGATTGCAATGCCGGAGGCAACCATGGAGATTGCACCGCCGGAGGCAGCCATGGAGATTCCAGTGCCGGATGT
| 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 | 74.30% | 4.00% | 12.87% | 8.82% | NA |
| All Indica | 2759 | 71.40% | 1.10% | 16.24% | 11.31% | NA |
| All Japonica | 1512 | 81.00% | 4.80% | 7.87% | 6.35% | NA |
| Aus | 269 | 75.50% | 10.80% | 11.52% | 2.23% | NA |
| Indica I | 595 | 52.30% | 0.70% | 25.04% | 22.02% | NA |
| Indica II | 465 | 69.00% | 0.90% | 20.65% | 9.46% | NA |
| Indica III | 913 | 84.40% | 1.30% | 8.87% | 5.37% | NA |
| Indica Intermediate | 786 | 72.10% | 1.10% | 15.52% | 11.20% | NA |
| Temperate Japonica | 767 | 91.50% | 6.00% | 0.65% | 1.83% | NA |
| Tropical Japonica | 504 | 66.30% | 0.80% | 19.25% | 13.69% | NA |
| Japonica Intermediate | 241 | 78.40% | 9.10% | 7.05% | 5.39% | NA |
| VI/Aromatic | 96 | 45.80% | 54.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 78.90% | 6.70% | 11.11% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216131209 | C -> DEL | LOC_Os12g27400.1 | N | frameshift_variant | Average:15.582; most accessible tissue: Callus, score: 32.847 | N | N | N | N |
| vg1216131209 | C -> T | LOC_Os12g27400.1 | missense_variant ; p.Glu311Lys; MODERATE | nonsynonymous_codon ; E311K | Average:15.582; most accessible tissue: Callus, score: 32.847 | unknown | unknown | TOLERATED | 0.06 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216131209 | NA | 2.95E-07 | mr1057 | 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 |
| vg1216131209 | 4.65E-06 | NA | mr1489 | 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 |
| vg1216131209 | 8.33E-08 | NA | mr1778 | 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 |
| vg1216131209 | NA | 1.36E-11 | 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 |
| vg1216131209 | 4.78E-08 | 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 |
| vg1216131209 | 1.39E-08 | 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 |