| Variant ID: vg0402811414 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2811414 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, C: 0.03, others allele: 0.00, population size: 232. )
AGATTGCTTGCAAGAAAGACGAGAATAGCTATGCACAAGTCTGGGAAAGGTACATCGACAAAACTCTGATGCAGGCTGCTGACGATAGGTTACAAGGTGC[G/C]
TTCGATAAGAGGCAGATGGAGCGTGTGATCGTCTTGGGGCTGTGGTGTTGTCAGCCTAATATTGAGATGCGACCTACGATGGAGAAAGCAATGGATTTCC
GGAAATCCATTGCTTTCTCCATCGTAGGTCGCATCTCAATATTAGGCTGACAACACCACAGCCCCAAGACGATCACACGCTCCATCTGCCTCTTATCGAA[C/G]
GCACCTTGTAACCTATCGTCAGCAGCCTGCATCAGAGTTTTGTCGATGTACCTTTCCCAGACTTGTGCATAGCTATTCTCGTCTTTCTTGCAAGCAATCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.10% | 3.60% | 0.30% | 3.07% | NA |
| All Indica | 2759 | 98.20% | 1.30% | 0.00% | 0.54% | NA |
| All Japonica | 1512 | 85.10% | 5.60% | 0.93% | 8.33% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.10% | 3.00% | 0.00% | 0.99% | NA |
| Indica Intermediate | 786 | 98.20% | 1.00% | 0.00% | 0.76% | NA |
| Temperate Japonica | 767 | 82.50% | 9.90% | 1.83% | 5.74% | NA |
| Tropical Japonica | 504 | 92.70% | 0.60% | 0.00% | 6.75% | NA |
| Japonica Intermediate | 241 | 77.60% | 2.50% | 0.00% | 19.92% | NA |
| VI/Aromatic | 96 | 58.30% | 40.60% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 87.80% | 8.90% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402811414 | G -> C | LOC_Os04g05560.1 | synonymous_variant ; p.Ala586Ala; LOW | synonymous_codon | Average:63.864; most accessible tissue: Zhenshan97 panicle, score: 83.904 | N | N | N | N |
| vg0402811414 | G -> DEL | LOC_Os04g05560.1 | N | frameshift_variant | Average:63.864; most accessible tissue: Zhenshan97 panicle, score: 83.904 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402811414 | 4.36E-10 | 8.67E-35 | Awn_length | All | YES | 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 |
| vg0402811414 | NA | 1.24E-11 | 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 |
| vg0402811414 | 7.13E-06 | NA | Heading_date | 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 |
| vg0402811414 | NA | 2.65E-06 | mr1549_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 |
| vg0402811414 | NA | 2.64E-06 | mr1757_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 |