| Variant ID: vg0113384484 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 13384484 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 119. )
CGAGTTCCAATGGAAACTGTTCTTATTATATTCGATTCCGTATCTGACAAAATATTTCTGAATTCATTTCCGTTTCCGAAAAATTCCGACCGGCTTATTC[T/C]
GTTTCCGAAAACATGCCCGGAATCTAGAAATATTCCGTACCGTTTTCATCCCAACCGCCCGTGCCTCTCCGCTGCCGGCACTCGTCCTCCACCCCATCCG
CGGATGGGGTGGAGGACGAGTGCCGGCAGCGGAGAGGCACGGGCGGTTGGGATGAAAACGGTACGGAATATTTCTAGATTCCGGGCATGTTTTCGGAAAC[A/G]
GAATAAGCCGGTCGGAATTTTTCGGAAACGGAAATGAATTCAGAAATATTTTGTCAGATACGGAATCGAATATAATAAGAACAGTTTCCATTGGAACTCG
| 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 | 84.60% | 14.20% | 1.14% | 0.00% | NA |
| All Indica | 2759 | 96.90% | 3.00% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 58.80% | 37.80% | 3.37% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 86.70% | 13.10% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.60% | 2.20% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 30.40% | 65.80% | 3.78% | 0.00% | NA |
| Tropical Japonica | 504 | 97.20% | 1.00% | 1.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 68.90% | 25.70% | 5.39% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 78.90% | 21.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0113384484 | T -> C | LOC_Os01g23790-LOC_Os01g23800 | intergenic_region ; MODIFIER | silent_mutation | Average:70.936; most accessible tissue: Zhenshan97 young leaf, score: 78.938 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0113384484 | NA | 6.57E-14 | 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 |
| vg0113384484 | NA | 7.76E-15 | 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 |
| vg0113384484 | NA | 4.41E-20 | Plant_height | 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 |
| vg0113384484 | 1.85E-06 | 2.58E-20 | Spikelet_length | 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 |
| vg0113384484 | 3.83E-06 | 3.10E-21 | Spikelet_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 |
| vg0113384484 | NA | 8.55E-09 | mr1002 | 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 |
| vg0113384484 | NA | 2.14E-08 | mr1002 | 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 |
| vg0113384484 | NA | 9.49E-06 | mr1010 | 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 |
| vg0113384484 | NA | 2.60E-08 | mr1013 | 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 |
| vg0113384484 | NA | 9.14E-08 | mr1031 | 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 |
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