| Variant ID: vg0703432101 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 3432101 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 322. )
CCTGAGTTACCAAAAAGCAAGTTATTCAGAAGAATTAGAAACTAAGATGAGAACAGAAGGTGTGCCTAAACAATAGAGAAAATCAATTCAAATGATGGAA[G/T]
AGTAGTAGTCGAGTAGATGACAGTGTGAAGAAAAATCAGATCAAGATCTATCTACAACCAGATGATTCTTATAAAAAAAATGAAGTATGCATATTGAATT
AATTCAATATGCATACTTCATTTTTTTTATAAGAATCATCTGGTTGTAGATAGATCTTGATCTGATTTTTCTTCACACTGTCATCTACTCGACTACTACT[C/A]
TTCCATCATTTGAATTGATTTTCTCTATTGTTTAGGCACACCTTCTGTTCTCATCTTAGTTTCTAATTCTTCTGAATAACTTGCTTTTTGGTAACTCAGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0703432101 | G -> T | LOC_Os07g06960.1 | upstream_gene_variant ; 3634.0bp to feature; MODIFIER | silent_mutation | Average:45.877; most accessible tissue: Zhenshan97 young leaf, score: 61.386 | N | N | N | N |
| vg0703432101 | G -> T | LOC_Os07g06980.1 | downstream_gene_variant ; 3832.0bp to feature; MODIFIER | silent_mutation | Average:45.877; most accessible tissue: Zhenshan97 young leaf, score: 61.386 | N | N | N | N |
| vg0703432101 | G -> T | LOC_Os07g06980.2 | downstream_gene_variant ; 3832.0bp to feature; MODIFIER | silent_mutation | Average:45.877; most accessible tissue: Zhenshan97 young leaf, score: 61.386 | N | N | N | N |
| vg0703432101 | G -> T | LOC_Os07g06970.1 | intron_variant ; MODIFIER | silent_mutation | Average:45.877; most accessible tissue: Zhenshan97 young leaf, score: 61.386 | N | N | N | N |