| Variant ID: vg0725419338 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25419338 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 107. )
TTGTGTGTATGAGACGAGGATGGTCTGTGCCGCGGTCCTTCTGTGTCTTGGCTTGATCAAGGGCTCGTGCCCAGGTCCTAGTCCTCAACTGGCTCGGGTC[G/A]
GGGCTAGTGCCTGGGGAGATCCACATGTCGAGACTGGCCAGGCCGGGAACGTGGTGACCGAGGGTTATGGGTGACCCGATTGTGGGTTTTTGCCGATTCC
GGAATCGGCAAAAACCCACAATCGGGTCACCCATAACCCTCGGTCACCACGTTCCCGGCCTGGCCAGTCTCGACATGTGGATCTCCCCAGGCACTAGCCC[C/T]
GACCCGAGCCAGTTGAGGACTAGGACCTGGGCACGAGCCCTTGATCAAGCCAAGACACAGAAGGACCGCGGCACAGACCATCCTCGTCTCATACACACAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.70% | 0.10% | 1.38% | 77.76% | NA |
| All Indica | 2759 | 1.50% | 0.30% | 1.52% | 96.74% | NA |
| All Japonica | 1512 | 59.50% | 0.00% | 0.66% | 39.88% | NA |
| Aus | 269 | 0.70% | 0.00% | 1.12% | 98.14% | NA |
| Indica I | 595 | 2.20% | 0.30% | 4.03% | 93.45% | NA |
| Indica II | 465 | 2.20% | 0.40% | 0.22% | 97.20% | NA |
| Indica III | 913 | 0.10% | 0.00% | 0.33% | 99.56% | NA |
| Indica Intermediate | 786 | 2.20% | 0.40% | 1.78% | 95.67% | NA |
| Temperate Japonica | 767 | 89.40% | 0.00% | 0.52% | 10.04% | NA |
| Tropical Japonica | 504 | 12.70% | 0.00% | 0.99% | 86.31% | NA |
| Japonica Intermediate | 241 | 61.80% | 0.00% | 0.41% | 37.76% | NA |
| VI/Aromatic | 96 | 12.50% | 0.00% | 1.04% | 86.46% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 10.00% | 62.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725419338 | G -> DEL | N | N | silent_mutation | Average:5.87; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |
| vg0725419338 | G -> A | LOC_Os07g42450.1 | upstream_gene_variant ; 3652.0bp to feature; MODIFIER | silent_mutation | Average:5.87; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |
| vg0725419338 | G -> A | LOC_Os07g42470.1 | upstream_gene_variant ; 3903.0bp to feature; MODIFIER | silent_mutation | Average:5.87; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |
| vg0725419338 | G -> A | LOC_Os07g42460.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.87; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |