| Variant ID: vg0219100137 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 19100137 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, G: 0.28, others allele: 0.00, population size: 263. )
ATTTTTGAAAACCAGAAACTAGAAACGGGAATGTTCAACTTAACAAGTCCAGGACTAAAATGGTTCATAAGAATAAAACATGAGTTTGTGCAATTTCCTA[G/C]
AGATGATCCCATGGATGATGGATCATGTAATTAAAACAACAGGATGAAATCACTAGCTGTTTAGGCAATCAACAGCAGAACATTAGCGAAGCTATGAGGT
ACCTCATAGCTTCGCTAATGTTCTGCTGTTGATTGCCTAAACAGCTAGTGATTTCATCCTGTTGTTTTAATTACATGATCCATCATCCATGGGATCATCT[C/G]
TAGGAAATTGCACAAACTCATGTTTTATTCTTATGAACCATTTTAGTCCTGGACTTGTTAAGTTGAACATTCCCGTTTCTAGTTTCTGGTTTTCAAAAAT
| 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 | 92.30% | 7.70% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 88.90% | 11.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 75.70% | 24.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 90.20% | 9.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 82.30% | 17.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0219100137 | G -> C | LOC_Os02g32340.1 | upstream_gene_variant ; 2721.0bp to feature; MODIFIER | silent_mutation | Average:61.677; most accessible tissue: Zhenshan97 flower, score: 75.194 | N | N | N | N |
| vg0219100137 | G -> C | LOC_Os02g32350.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.677; most accessible tissue: Zhenshan97 flower, score: 75.194 | N | N | N | N |
| vg0219100137 | G -> C | LOC_Os02g32350.2 | intron_variant ; MODIFIER | silent_mutation | Average:61.677; most accessible tissue: Zhenshan97 flower, score: 75.194 | N | N | N | N |