| Variant ID: vg0818940169 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 18940169 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, A: 0.35, others allele: 0.00, population size: 84. )
GAATTTGCAAAGCTTGCATGATTCACATTTTCTAGTGACTAGGGGAATATGGAAGTACGTACTCTCTCTCTCTTATTATCATGTACTCACTCTCCCCTTC[A/T]
CATAGTCTAGGTTGAAGAAAATGAAGGATAGGCCATGTCCCTACACCTAAGCCATTGAAAGTACTCACCCTTATATTGTTGTTGTGAAAGACCAAGAACG
CGTTCTTGGTCTTTCACAACAACAATATAAGGGTGAGTACTTTCAATGGCTTAGGTGTAGGGACATGGCCTATCCTTCATTTTCTTCAACCTAGACTATG[T/A]
GAAGGGGAGAGTGAGTACATGATAATAAGAGAGAGAGAGTACGTACTTCCATATTCCCCTAGTCACTAGAAAATGTGAATCATGCAAGCTTTGCAAATTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.40% | 35.80% | 0.53% | 18.22% | NA |
| All Indica | 2759 | 67.30% | 7.50% | 0.80% | 24.39% | NA |
| All Japonica | 1512 | 1.70% | 86.60% | 0.07% | 11.71% | NA |
| Aus | 269 | 80.30% | 18.60% | 0.00% | 1.12% | NA |
| Indica I | 595 | 77.80% | 16.10% | 0.34% | 5.71% | NA |
| Indica II | 465 | 88.60% | 4.10% | 0.65% | 6.67% | NA |
| Indica III | 913 | 52.50% | 4.40% | 0.88% | 42.28% | NA |
| Indica Intermediate | 786 | 63.90% | 6.70% | 1.15% | 28.24% | NA |
| Temperate Japonica | 767 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.80% | 64.90% | 0.20% | 32.14% | NA |
| Japonica Intermediate | 241 | 2.10% | 91.70% | 0.00% | 6.22% | NA |
| VI/Aromatic | 96 | 7.30% | 87.50% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 46.70% | 47.80% | 1.11% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0818940169 | A -> T | LOC_Os08g30710.1 | intron_variant ; MODIFIER | silent_mutation | Average:29.789; most accessible tissue: Zhenshan97 young leaf, score: 49.329 | N | N | N | N |
| vg0818940169 | A -> DEL | N | N | silent_mutation | Average:29.789; most accessible tissue: Zhenshan97 young leaf, score: 49.329 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0818940169 | NA | 4.78E-06 | Spikelet_length | Ind_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 |
| vg0818940169 | NA | 6.22E-06 | mr1639 | 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 |