| Variant ID: vg1226938080 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 26938080 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.12, others allele: 0.00, population size: 94. )
GCCTCTATCACTGGTGGAGAAATTGTTTGTAGTCCCGGTTCGTAACCCCCCTTTAGTTCCGGTTGTCCAACCGGGACTACGAATCCGGGACTAAAGATAG[C/T]
GATCTTTAGTACCGGGTGAAATAACCGGGACTAAAGATCGATCTTTAGTCCCGGTTGGTAACACGAACCGGGACTAAAGATCGGTCAGCCACGTGGCCGG
CCGGCCACGTGGCTGACCGATCTTTAGTCCCGGTTCGTGTTACCAACCGGGACTAAAGATCGATCTTTAGTCCCGGTTATTTCACCCGGTACTAAAGATC[G/A]
CTATCTTTAGTCCCGGATTCGTAGTCCCGGTTGGACAACCGGAACTAAAGGGGGGTTACGAACCGGGACTACAAACAATTTCTCCACCAGTGATAGAGGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.30% | 12.70% | 0.83% | 39.25% | NA |
| All Indica | 2759 | 78.10% | 3.10% | 0.47% | 18.38% | NA |
| All Japonica | 1512 | 2.00% | 14.50% | 1.32% | 82.21% | NA |
| Aus | 269 | 1.10% | 96.70% | 0.00% | 2.23% | NA |
| Indica I | 595 | 37.50% | 5.90% | 1.34% | 55.29% | NA |
| Indica II | 465 | 94.40% | 0.90% | 0.43% | 4.30% | NA |
| Indica III | 913 | 91.90% | 1.20% | 0.11% | 6.79% | NA |
| Indica Intermediate | 786 | 83.10% | 4.50% | 0.25% | 12.21% | NA |
| Temperate Japonica | 767 | 1.80% | 25.70% | 1.43% | 71.06% | NA |
| Tropical Japonica | 504 | 2.00% | 2.40% | 1.59% | 94.05% | NA |
| Japonica Intermediate | 241 | 2.50% | 4.10% | 0.41% | 92.95% | NA |
| VI/Aromatic | 96 | 4.20% | 19.80% | 3.12% | 72.92% | NA |
| Intermediate | 90 | 47.80% | 16.70% | 3.33% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1226938080 | C -> DEL | N | N | silent_mutation | Average:23.651; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg1226938080 | C -> T | LOC_Os12g43410.1 | upstream_gene_variant ; 4788.0bp to feature; MODIFIER | silent_mutation | Average:23.651; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg1226938080 | C -> T | LOC_Os12g43410-LOC_Os12g43440 | intergenic_region ; MODIFIER | silent_mutation | Average:23.651; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1226938080 | NA | 1.91E-06 | mr1201 | 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 |
| vg1226938080 | NA | 1.02E-09 | mr1662 | 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 |
| vg1226938080 | NA | 1.92E-08 | mr1662_2 | 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 |
| vg1226938080 | 3.74E-06 | 2.15E-08 | mr1745_2 | Ind_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 |