| Variant ID: vg1209004546 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004546 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 51. )
GTGTGACCAACCAACCGTGTAGGCGAGGACACTAGTTGACAGTGGACGAGGCGGCCGGTCAGTGAAGACGATGATGTCCATCAGCAGCGGCGCAATATGC[C/T]
AGCCGTGAAGGCGAAGAGGCTTGTCGACGGAAGATGAGGCAGCTGGCAGTGTAGAATATGTCATTATCAGCCATGGCGATAAAGACAACATGTTTGGATA
TATCCAAACATGTTGTCTTTATCGCCATGGCTGATAATGACATATTCTACACTGCCAGCTGCCTCATCTTCCGTCGACAAGCCTCTTCGCCTTCACGGCT[G/A]
GCATATTGCGCCGCTGCTGATGGACATCATCGTCTTCACTGACCGGCCGCCTCGTCCACTGTCAACTAGTGTCCTCGCCTACACGGTTGGTTGGTCACAC
| 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 | 39.70% | 38.10% | 0.51% | 21.67% | NA |
| All Indica | 2759 | 54.00% | 10.40% | 0.76% | 34.83% | NA |
| All Japonica | 1512 | 4.40% | 94.50% | 0.00% | 1.06% | NA |
| Aus | 269 | 81.00% | 5.20% | 0.74% | 13.01% | NA |
| Indica I | 595 | 36.10% | 21.70% | 0.67% | 41.51% | NA |
| Indica II | 465 | 51.60% | 12.50% | 0.65% | 35.27% | NA |
| Indica III | 913 | 65.30% | 2.20% | 0.55% | 31.98% | NA |
| Indica Intermediate | 786 | 55.70% | 10.30% | 1.15% | 32.82% | NA |
| Temperate Japonica | 767 | 6.00% | 93.00% | 0.00% | 1.04% | NA |
| Tropical Japonica | 504 | 3.60% | 95.60% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 1.20% | 97.10% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 72.90% | 22.90% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 36.70% | 53.30% | 1.11% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004546 | C -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:46.019; most accessible tissue: Callus, score: 82.589 | N | N | N | N |
| vg1209004546 | C -> T | LOC_Os12g15770.1 | stop_gained ; p.Trp31*; HIGH | stop_gained | Average:46.019; most accessible tissue: Callus, score: 82.589 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209004546 | NA | 4.22E-09 | mr1425 | 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 |
| vg1209004546 | NA | 1.43E-06 | mr1425 | 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 |
| vg1209004546 | NA | 4.45E-06 | mr1574 | 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 |
| vg1209004546 | NA | 1.54E-07 | mr1659 | 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 |