| Variant ID: vg0402942194 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2942194 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, A: 0.05, others allele: 0.00, population size: 78. )
AATTCAATCAGAGAGAGATTTTTTTTTCTCTCGAATTTTACTAAGCGGAGAACGAATGAGATAAACTAGATTAAAACTCTCGTTGTTCCCAACTCATAAA[C/A]
CCTAGGTTCTTATCATATAAGAACAGTGGATTAAGAAGTAAATTGGGGAAAATAGTGGATAAACTAGATTGAAATTCCCCAGTGTTAAGCAGAAGGGAAT
ATTCCCTTCTGCTTAACACTGGGGAATTTCAATCTAGTTTATCCACTATTTTCCCCAATTTACTTCTTAATCCACTGTTCTTATATGATAAGAACCTAGG[G/T]
TTTATGAGTTGGGAACAACGAGAGTTTTAATCTAGTTTATCTCATTCGTTCTCCGCTTAGTAAAATTCGAGAGAAAAAAAAATCTCTCTCTGATTGAATT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.50% | 37.60% | 0.99% | 9.88% | NA |
| All Indica | 2759 | 29.70% | 54.00% | 1.01% | 15.33% | NA |
| All Japonica | 1512 | 90.60% | 6.50% | 0.93% | 1.92% | NA |
| Aus | 269 | 56.10% | 39.40% | 0.37% | 4.09% | NA |
| Indica I | 595 | 9.10% | 90.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 24.90% | 53.50% | 1.08% | 20.43% | NA |
| Indica III | 913 | 40.50% | 34.90% | 1.10% | 23.44% | NA |
| Indica Intermediate | 786 | 35.50% | 48.30% | 1.65% | 14.50% | NA |
| Temperate Japonica | 767 | 93.90% | 1.60% | 1.43% | 3.13% | NA |
| Tropical Japonica | 504 | 83.10% | 15.90% | 0.20% | 0.79% | NA |
| Japonica Intermediate | 241 | 95.90% | 2.90% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 50.00% | 49.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 53.30% | 38.90% | 3.33% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402942194 | C -> DEL | N | N | silent_mutation | Average:29.542; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | N | N | N | N |
| vg0402942194 | C -> A | LOC_Os04g05750.1 | downstream_gene_variant ; 282.0bp to feature; MODIFIER | silent_mutation | Average:29.542; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | N | N | N | N |
| vg0402942194 | C -> A | LOC_Os04g05740-LOC_Os04g05750 | intergenic_region ; MODIFIER | silent_mutation | Average:29.542; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402942194 | 4.50E-06 | 2.78E-08 | 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 |
| vg0402942194 | 2.65E-08 | 2.65E-08 | mr1698 | 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 |
| vg0402942194 | NA | 3.32E-07 | mr1798_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 |