| Variant ID: vg0903406850 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 3406850 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, T: 0.14, others allele: 0.00, population size: 195. )
GGATACATACCACAAATTAGATCCTACCATTGGTTTAGCAAGGTCTCCATATTTACCAGGTTCAATAGGCGTGTAGCACTGTGATGTTTTTTCTTCCAGG[G/T]
ATTAACTCAGGAACAAATTAATGGATGATAAAAAAATAATAAAGAGAAAATTAAACTTACATCAATTGCTTCATGCATGTCAGGTTTACCCTTGGTAATA
TATTACCAAGGGTAAACCTGACATGCATGAAGCAATTGATGTAAGTTTAATTTTCTCTTTATTATTTTTTTATCATCCATTAATTTGTTCCTGAGTTAAT[C/A]
CCTGGAAGAAAAAACATCACAGTGCTACACGCCTATTGAACCTGGTAAATATGGAGACCTTGCTAAACCAATGGTAGGATCTAATTTGTGGTATGTATCC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.90% | 37.00% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 95.90% | 4.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 0.90% | 99.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 91.60% | 8.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 7.30% | 92.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 43.30% | 55.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0903406850 | G -> T | LOC_Os09g07010.1 | upstream_gene_variant ; 3741.0bp to feature; MODIFIER | silent_mutation | Average:54.109; most accessible tissue: Zhenshan97 young leaf, score: 70.177 | N | N | N | N |
| vg0903406850 | G -> T | LOC_Os09g07030.1 | downstream_gene_variant ; 2030.0bp to feature; MODIFIER | silent_mutation | Average:54.109; most accessible tissue: Zhenshan97 young leaf, score: 70.177 | N | N | N | N |
| vg0903406850 | G -> T | LOC_Os09g07020.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.109; most accessible tissue: Zhenshan97 young leaf, score: 70.177 | N | N | N | N |
| vg0903406850 | G -> T | LOC_Os09g07020.2 | intron_variant ; MODIFIER | silent_mutation | Average:54.109; most accessible tissue: Zhenshan97 young leaf, score: 70.177 | N | N | N | N |