| Variant ID: vg0407628826 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 7628826 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.16, others allele: 0.00, population size: 76. )
GTGCTACCGGTGGTCCTATAGGAAATCAAGGCGATAACCCTCAAGAAGTGCACGGAGCTCCAAGTGATGTTGCTCAAGGGCTGCAAGGAGGAAATCTTAA[C/T]
CAGAATATTGAGCTAGCACAAGATTTTTTCAACAACTTTCAGGATCGGGTTGATTACGCGGTGCATCATGCTTTGATCAATCAATCCGGGGTCTTAGTCA
TGACTAAGACCCCGGATTGATTGATCAAAGCATGATGCACCGCGTAATCAACCCGATCCTGAAAGTTGTTGAAAAAATCTTGTGCTAGCTCAATATTCTG[G/A]
TTAAGATTTCCTCCTTGCAGCCCTTGAGCAACATCACTTGGAGCTCCGTGCACTTCTTGAGGGTTATCGCCTTGATTTCCTATAGGACCACCGGTAGCAC
| 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 | 35.60% | 10.30% | 5.54% | 48.50% | NA |
| All Indica | 2759 | 3.50% | 17.50% | 8.30% | 70.64% | NA |
| All Japonica | 1512 | 98.50% | 0.10% | 0.07% | 1.39% | NA |
| Aus | 269 | 0.70% | 0.00% | 3.35% | 95.91% | NA |
| Indica I | 595 | 2.70% | 2.00% | 4.87% | 90.42% | NA |
| Indica II | 465 | 4.90% | 29.20% | 7.74% | 58.06% | NA |
| Indica III | 913 | 2.00% | 20.70% | 9.97% | 67.36% | NA |
| Indica Intermediate | 786 | 5.10% | 18.70% | 9.29% | 66.92% | NA |
| Temperate Japonica | 767 | 99.50% | 0.10% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 97.20% | 0.00% | 0.20% | 2.58% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 52.10% | 0.00% | 19.79% | 28.12% | NA |
| Intermediate | 90 | 51.10% | 3.30% | 4.44% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0407628826 | C -> DEL | LOC_Os04g13660.1 | N | frameshift_variant | Average:16.0; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
| vg0407628826 | C -> T | LOC_Os04g13660.1 | synonymous_variant ; p.Asn141Asn; LOW | synonymous_codon | Average:16.0; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0407628826 | NA | 7.23E-07 | 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 |
| vg0407628826 | 4.39E-06 | NA | mr1425_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 |
| vg0407628826 | NA | 1.03E-07 | mr1425_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 |
| vg0407628826 | NA | 3.15E-08 | mr1446_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 |