| Variant ID: vg0824000142 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 24000142 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 241. )
GGAATCCATCATCGTTCATGCTGGATGGATGGATGGATGTAGTGAATGGTAGTTTTTCTTATTTTTGTTGGAGATGGATATTTTTTACTTTACATCTAAT[C/A]
GGATATATGTTGTCTTTTAAATTGAGAATTTAGCTACTCAAACAATCCATTCTGAAATTCGTTCAAACGAAGATTTGAACTTAAGTATCTTAGGCTGCGT
ACGCAGCCTAAGATACTTAAGTTCAAATCTTCGTTTGAACGAATTTCAGAATGGATTGTTTGAGTAGCTAAATTCTCAATTTAAAAGACAACATATATCC[G/T]
ATTAGATGTAAAGTAAAAAATATCCATCTCCAACAAAAATAAGAAAAACTACCATTCACTACATCCATCCATCCATCCAGCATGAACGATGATGGATTCC
| 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 | 97.30% | 1.70% | 1.04% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.00% | 0.51% | 0.00% | NA |
| All Japonica | 1512 | 92.70% | 5.10% | 2.25% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.00% | 0.84% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.00% | 0.65% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.10% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 85.80% | 9.90% | 4.30% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0824000142 | C -> A | LOC_Os08g37890.1 | 3_prime_UTR_variant ; 546.0bp to feature; MODIFIER | silent_mutation | Average:71.519; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0824000142 | C -> A | LOC_Os08g37904.1 | upstream_gene_variant ; 2731.0bp to feature; MODIFIER | silent_mutation | Average:71.519; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0824000142 | C -> A | LOC_Os08g37904.4 | upstream_gene_variant ; 2725.0bp to feature; MODIFIER | silent_mutation | Average:71.519; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0824000142 | C -> A | LOC_Os08g37904.6 | upstream_gene_variant ; 2731.0bp to feature; MODIFIER | silent_mutation | Average:71.519; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0824000142 | C -> A | LOC_Os08g37904.3 | upstream_gene_variant ; 2731.0bp to feature; MODIFIER | silent_mutation | Average:71.519; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0824000142 | C -> A | LOC_Os08g37904.2 | upstream_gene_variant ; 2731.0bp to feature; MODIFIER | silent_mutation | Average:71.519; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0824000142 | C -> A | LOC_Os08g37904.5 | upstream_gene_variant ; 2731.0bp to feature; MODIFIER | silent_mutation | Average:71.519; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0824000142 | C -> A | LOC_Os08g37874.1 | downstream_gene_variant ; 3681.0bp to feature; MODIFIER | silent_mutation | Average:71.519; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0824000142 | C -> A | LOC_Os08g37874.3 | downstream_gene_variant ; 4399.0bp to feature; MODIFIER | silent_mutation | Average:71.519; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0824000142 | C -> A | LOC_Os08g37874.2 | downstream_gene_variant ; 3848.0bp to feature; MODIFIER | silent_mutation | Average:71.519; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0824000142 | 9.59E-19 | 2.94E-28 | Awn_length | Jap_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 |
| vg0824000142 | NA | 3.28E-10 | Heading_date | 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 |
| vg0824000142 | NA | 1.61E-07 | mr1156_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 |
| vg0824000142 | NA | 6.54E-07 | 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 |
| vg0824000142 | NA | 6.78E-09 | mr1624_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 |
| vg0824000142 | NA | 5.05E-07 | mr1733_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 |
| vg0824000142 | NA | 1.92E-07 | 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 |