| Variant ID: vg0315244547 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15244547 |
| Reference Allele: T | Alternative Allele: C |
| 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: 92. )
AATCATCGGCTGTAATTGTAGCAACTTCTATCTCAACATCTTTCAACATTGGCTTATATCCTGATGCCCCTTGAGCCAAATCATTAGCCTCAACATTCTG[T/C]
TCTCGTGATACATGTTTCAAAGTTACGAGCCGAAATCCACTCATCAATTCTCGGCACTTTTCATTGTAAACCATCAATGTATCATTCTTGCATTCATATT
AATATGAATGCAAGAATGATACATTGATGGTTTACAATGAAAAGTGCCGAGAATTGATGAGTGGATTTCGGCTCGTAACTTTGAAACATGTATCACGAGA[A/G]
CAGAATGTTGAGGCTAATGATTTGGCTCAAGGGGCATCAGGATATAAGCCAATGTTGAAAGATGTTGAGATAGAAGTTGCTACAATTACAGCCGATGATT
| 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 | 29.90% | 28.20% | 8.27% | 33.60% | NA |
| All Indica | 2759 | 24.80% | 18.30% | 11.20% | 45.78% | NA |
| All Japonica | 1512 | 35.20% | 52.40% | 4.17% | 8.27% | NA |
| Aus | 269 | 28.30% | 2.20% | 3.35% | 66.17% | NA |
| Indica I | 595 | 16.50% | 34.30% | 13.61% | 35.63% | NA |
| Indica II | 465 | 9.50% | 23.00% | 14.84% | 52.69% | NA |
| Indica III | 913 | 37.80% | 7.00% | 6.68% | 48.52% | NA |
| Indica Intermediate | 786 | 24.90% | 16.40% | 12.47% | 46.18% | NA |
| Temperate Japonica | 767 | 6.10% | 84.60% | 2.61% | 6.65% | NA |
| Tropical Japonica | 504 | 70.60% | 16.50% | 4.37% | 8.53% | NA |
| Japonica Intermediate | 241 | 53.50% | 24.90% | 8.71% | 12.86% | NA |
| VI/Aromatic | 96 | 85.40% | 7.30% | 2.08% | 5.21% | NA |
| Intermediate | 90 | 45.60% | 26.70% | 8.89% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0315244547 | T -> C | LOC_Os03g26704.1 | synonymous_variant ; p.Glu986Glu; LOW | synonymous_codon | Average:13.556; most accessible tissue: Callus, score: 53.11 | N | N | N | N |
| vg0315244547 | T -> DEL | LOC_Os03g26704.1 | N | frameshift_variant | Average:13.556; most accessible tissue: Callus, score: 53.11 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0315244547 | NA | 4.81E-06 | mr1177 | 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 |
| vg0315244547 | NA | 3.20E-06 | mr1729 | 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 |
| vg0315244547 | NA | 1.01E-09 | mr1578_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 |
| vg0315244547 | NA | 9.41E-06 | mr1853_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 |
| vg0315244547 | NA | 3.02E-10 | mr1952_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 |