| Variant ID: vg1214406518 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 14406518 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCTTTGTGTGCGGTAAGCCTAGGCATTGGGCCAAGAATTGTCCTAATCGCAAGGACAAGAAGTCTGCCAACATGGTTATTAGCGAGGGCGGAGGAACATC[G/A]
GGGTATGGTAAATTTTTACCTACAATTCTCTCTGTTTTTCATTCACCTGATTGGTGGGTTGATACTGGTGCTAATATTCATGTGTGTGCTGATATTTCCA
TGGAAATATCAGCACACACATGAATATTAGCACCAGTATCAACCCACCAATCAGGTGAATGAAAAACAGAGAGAATTGTAGGTAAAAATTTACCATACCC[C/T]
GATGTTCCTCCGCCCTCGCTAATAACCATGTTGGCAGACTTCTTGTCCTTGCGATTAGGACAATTCTTGGCCCAATGCCTAGGCTTACCGCACACAAAGC
| 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 | 81.70% | 9.90% | 0.87% | 7.60% | NA |
| All Indica | 2759 | 69.90% | 16.00% | 1.41% | 12.69% | NA |
| All Japonica | 1512 | 98.80% | 0.70% | 0.07% | 0.40% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 34.30% | 22.70% | 3.03% | 40.00% | NA |
| Indica II | 465 | 90.80% | 5.80% | 0.22% | 3.23% | NA |
| Indica III | 913 | 80.70% | 16.00% | 0.88% | 2.41% | NA |
| Indica Intermediate | 786 | 71.90% | 17.00% | 1.53% | 9.54% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 97.20% | 2.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 11.10% | 1.11% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1214406518 | G -> DEL | LOC_Os12g25080.1 | N | frameshift_variant | Average:20.623; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg1214406518 | G -> A | LOC_Os12g25080.1 | synonymous_variant ; p.Ser182Ser; LOW | synonymous_codon | Average:20.623; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1214406518 | 8.75E-06 | NA | mr1005 | 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 |
| vg1214406518 | 7.90E-07 | 7.37E-06 | mr1005 | 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 |
| vg1214406518 | NA | 1.73E-06 | mr1007 | 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 |
| vg1214406518 | NA | 3.12E-06 | mr1336 | 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 |
| vg1214406518 | 5.56E-06 | NA | mr1719 | 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 |