| Variant ID: vg1209407906 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9407906 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 107. )
CCAATATTATCACACCATACCTTAGCAATTTTGGGTGCCTGAATTCCCAGTAGCATTAGCCAAAGCCTTATATTCTGCCTCTGTACTAGATCTGGATACA[G/A]
TAGCTTGCTTGCGTGCACTCCATGACACAAGATTAGGCCCTATAAAAACAGCAAAACCCCCAGTAGAACGCCGATCATCCAAACATCCTGCCCAATCTGC
GCAGATTGGGCAGGATGTTTGGATGATCGGCGTTCTACTGGGGGTTTTGCTGTTTTTATAGGGCCTAATCTTGTGTCATGGAGTGCACGCAAGCAAGCTA[C/T]
TGTATCCAGATCTAGTACAGAGGCAGAATATAAGGCTTTGGCTAATGCTACTGGGAATTCAGGCACCCAAAATTGCTAAGGTATGGTGTGATAATATTGG
| 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 | 69.50% | 7.90% | 4.70% | 17.88% | NA |
| All Indica | 2759 | 58.50% | 13.10% | 7.03% | 21.38% | NA |
| All Japonica | 1512 | 83.40% | 0.30% | 0.93% | 15.34% | NA |
| Aus | 269 | 97.80% | 0.70% | 1.49% | 0.00% | NA |
| Indica I | 595 | 52.40% | 14.30% | 6.72% | 26.55% | NA |
| Indica II | 465 | 60.90% | 16.80% | 8.82% | 13.55% | NA |
| Indica III | 913 | 67.40% | 8.00% | 4.93% | 19.72% | NA |
| Indica Intermediate | 786 | 51.30% | 16.00% | 8.65% | 24.05% | NA |
| Temperate Japonica | 767 | 91.10% | 0.50% | 0.91% | 7.43% | NA |
| Tropical Japonica | 504 | 76.80% | 0.20% | 0.79% | 22.22% | NA |
| Japonica Intermediate | 241 | 72.60% | 0.00% | 1.24% | 26.14% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 6.25% | 9.38% | NA |
| Intermediate | 90 | 75.60% | 4.40% | 4.44% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209407906 | G -> DEL | LOC_Os12g16430.1 | N | frameshift_variant | Average:27.929; most accessible tissue: Minghui63 root, score: 55.188 | N | N | N | N |
| vg1209407906 | G -> A | LOC_Os12g16430.1 | missense_variant ; p.Thr1177Ile; MODERATE | nonsynonymous_codon ; T1177I | Average:27.929; most accessible tissue: Minghui63 root, score: 55.188 | unknown | unknown | DELETERIOUS | 0.03 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209407906 | NA | 9.32E-06 | mr1452_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 |
| vg1209407906 | 3.81E-06 | NA | mr1568_2 | 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 |
| vg1209407906 | 3.51E-06 | 3.03E-07 | mr1568_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 |
| vg1209407906 | NA | 8.55E-06 | mr1622_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 |
| vg1209407906 | NA | 2.10E-06 | mr1864_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 |