| Variant ID: vg1208638605 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8638605 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 93. )
GTTGATCATCGGACATGGCATTAAATAAAACAAGAACAGAAGACTTCGATGAAGAAGCACCAACATCCAAAGAAGTTGAAGATGAAACCAAAGCACTAGA[C/T]
TTAGAATCACTTTTACGAGAAAGAATATTCATCTCATGAGTTTTCAGTTTTGTGTAAAGCGAATCCAAAGTCAAAGTAGACATGTTAACAGACTCCTGAA
TTCAGGAGTCTGTTAACATGTCTACTTTGACTTTGGATTCGCTTTACACAAAACTGAAAACTCATGAGATGAATATTCTTTCTCGTAAAAGTGATTCTAA[G/A]
TCTAGTGCTTTGGTTTCATCTTCAACTTCTTTGGATGTTGGTGCTTCTTCATCGAAGTCTTCTGTTCTTGTTTTATTTAATGCCATGTCCGATGATCAAC
| 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 | 44.40% | 20.40% | 26.45% | 8.76% | NA |
| All Indica | 2759 | 40.70% | 26.00% | 30.59% | 2.75% | NA |
| All Japonica | 1512 | 55.20% | 4.30% | 18.39% | 22.09% | NA |
| Aus | 269 | 21.90% | 54.30% | 23.79% | 0.00% | NA |
| Indica I | 595 | 71.60% | 12.30% | 15.29% | 0.84% | NA |
| Indica II | 465 | 37.00% | 25.80% | 32.47% | 4.73% | NA |
| Indica III | 913 | 18.00% | 35.70% | 43.15% | 3.18% | NA |
| Indica Intermediate | 786 | 45.80% | 25.20% | 26.46% | 2.54% | NA |
| Temperate Japonica | 767 | 81.10% | 0.10% | 4.95% | 13.82% | NA |
| Tropical Japonica | 504 | 22.20% | 11.70% | 33.13% | 32.94% | NA |
| Japonica Intermediate | 241 | 41.90% | 2.10% | 30.29% | 25.73% | NA |
| VI/Aromatic | 96 | 33.30% | 25.00% | 39.58% | 2.08% | NA |
| Intermediate | 90 | 54.40% | 14.40% | 28.89% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208638605 | C -> DEL | LOC_Os12g15140.1 | N | frameshift_variant | Average:12.055; most accessible tissue: Callus, score: 25.523 | N | N | N | N |
| vg1208638605 | C -> T | LOC_Os12g15140.1 | synonymous_variant ; p.Lys312Lys; LOW | synonymous_codon | Average:12.055; most accessible tissue: Callus, score: 25.523 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208638605 | NA | 4.03E-07 | mr1047_2 | 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 |
| vg1208638605 | NA | 2.96E-06 | mr1268_2 | 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 |
| vg1208638605 | NA | 7.08E-06 | mr1449_2 | 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 |
| vg1208638605 | NA | 3.31E-07 | mr1553_2 | 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 |
| vg1208638605 | 2.66E-06 | 2.65E-06 | mr1574_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 |
| vg1208638605 | NA | 7.86E-07 | mr1870_2 | 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 |