| Variant ID: vg0200603442 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 603442 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 66. )
CATTTCCAGAGGTATGAACCTGCATCGGTATTTTAAGTTCCATTACCGATAATCCATGTGTCCCAGCAAATCTCTTGGAAATGAAAGAATGCGAGGCACC[C/T]
GAATCAAAAAGAACTGTTGCTGGATATGAGTTCACTGGAAACGTGCCCAGCACGACATCTGATGCTGCCTGTGCTTCCTCTGCAGACACATGATTGGCGC
GCGCCAATCATGTGTCTGCAGAGGAAGCACAGGCAGCATCAGATGTCGTGCTGGGCACGTTTCCAGTGAACTCATATCCAGCAACAGTTCTTTTTGATTC[G/A]
GGTGCCTCGCATTCTTTCATTTCCAAGAGATTTGCTGGGACACATGGATTATCGGTAATGGAACTTAAAATACCGATGCAGGTTCATACCTCTGGAAATG
| 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 | 56.30% | 4.90% | 23.95% | 14.85% | NA |
| All Indica | 2759 | 34.50% | 5.80% | 35.09% | 24.57% | NA |
| All Japonica | 1512 | 96.40% | 0.10% | 2.71% | 0.86% | NA |
| Aus | 269 | 50.90% | 23.00% | 24.91% | 1.12% | NA |
| Indica I | 595 | 7.90% | 5.20% | 46.89% | 40.00% | NA |
| Indica II | 465 | 40.40% | 7.30% | 32.90% | 19.35% | NA |
| Indica III | 913 | 52.10% | 4.60% | 26.07% | 17.20% | NA |
| Indica Intermediate | 786 | 30.80% | 6.70% | 37.91% | 24.55% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 94.40% | 0.00% | 4.56% | 0.99% | NA |
| Japonica Intermediate | 241 | 89.60% | 0.40% | 7.05% | 2.90% | NA |
| VI/Aromatic | 96 | 54.20% | 5.20% | 40.62% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 2.20% | 18.89% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0200603442 | C -> T | LOC_Os02g02060.1 | synonymous_variant ; p.Ser410Ser; LOW | synonymous_codon | Average:12.719; most accessible tissue: Callus, score: 33.549 | N | N | N | N |
| vg0200603442 | C -> DEL | LOC_Os02g02060.1 | N | frameshift_variant | Average:12.719; most accessible tissue: Callus, score: 33.549 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0200603442 | NA | 5.58E-15 | mr1535 | 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 |
| vg0200603442 | NA | 1.35E-07 | mr1399_2 | 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 |
| vg0200603442 | NA | 4.38E-07 | mr1479_2 | 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 |
| vg0200603442 | NA | 7.08E-06 | mr1677_2 | 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 |
| vg0200603442 | NA | 2.16E-06 | mr1892_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 |