| Variant ID: vg0402980906 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2980906 |
| 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: 62. )
AGCAAAATGGCACTGCAAAGTTGCTTCGCATGGCGTCCTTAATTATTTGGGATGAAGCTGCAATGACGAAGCGTCAGGCAGTTGAGACTCTTGATAGATC[C/T]
CTTCAAGACATTATGGGTTGTTCATTGCCATTTGGAGGTAATGTCATTGTATTTGGTGGTGATTTCAGACAAGTTCTTCCCGTGGTGACACGTGGGACAA
TTGTCCCACGTGTCACCACGGGAAGAACTTGTCTGAAATCACCACCAAATACAATGACATTACCTCCAAATGGCAATGAACAACCCATAATGTCTTGAAG[G/A]
GATCTATCAAGAGTCTCAACTGCCTGACGCTTCGTCATTGCAGCTTCATCCCAAATAATTAAGGACGCCATGCGAAGCAACTTTGCAGTGCCATTTTGCT
| 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 | 84.70% | 0.50% | 0.57% | 14.28% | NA |
| All Indica | 2759 | 99.10% | 0.00% | 0.07% | 0.80% | NA |
| All Japonica | 1512 | 56.90% | 1.40% | 1.59% | 40.08% | NA |
| Aus | 269 | 98.10% | 0.00% | 0.37% | 1.49% | NA |
| Indica I | 595 | 97.80% | 0.20% | 0.17% | 1.85% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.00% | 0.43% | NA |
| Indica III | 913 | 99.70% | 0.00% | 0.00% | 0.33% | NA |
| Indica Intermediate | 786 | 99.10% | 0.00% | 0.13% | 0.76% | NA |
| Temperate Japonica | 767 | 83.60% | 2.20% | 2.48% | 11.73% | NA |
| Tropical Japonica | 504 | 21.20% | 0.00% | 0.60% | 78.17% | NA |
| Japonica Intermediate | 241 | 46.90% | 1.70% | 0.83% | 50.62% | NA |
| VI/Aromatic | 96 | 63.50% | 0.00% | 0.00% | 36.46% | NA |
| Intermediate | 90 | 90.00% | 1.10% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402980906 | C -> DEL | LOC_Os04g05800.1 | N | frameshift_variant | Average:14.236; most accessible tissue: Callus, score: 29.302 | N | N | N | N |
| vg0402980906 | C -> T | LOC_Os04g05800.1 | synonymous_variant ; p.Ser800Ser; LOW | synonymous_codon | Average:14.236; most accessible tissue: Callus, score: 29.302 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402980906 | 2.22E-06 | 4.87E-09 | Awn_length | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0402980906 | 3.43E-06 | 3.43E-06 | mr1464 | 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 |