| Variant ID: vg0704650141 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4650141 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.02, others allele: 0.00, population size: 327. )
AACTCATTAGTATCAACCAAGCTGATTGAATTGGCCTCATCACTGACCTCCAATGTGTTGGGGACAGATTTAGTGTTGGTGCTTTTAGCTGTCACCACTC[T/A]
GGTGATACCAACGCTCGTGATTGACTCAAGCTTGATGTTGCGGCATGTCACAAGCATGTTGTTGAGCGTGGCAATAATCTTGGCACACAACTCCTGGAAT
ATTCCAGGAGTTGTGTGCCAAGATTATTGCCACGCTCAACAACATGCTTGTGACATGCCGCAACATCAAGCTTGAGTCAATCACGAGCGTTGGTATCACC[A/T]
GAGTGGTGACAGCTAAAAGCACCAACACTAAATCTGTCCCCAACACATTGGAGGTCAGTGATGAGGCCAATTCAATCAGCTTGGTTGATACTAATGAGTT
| 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 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704650141 | T -> A | LOC_Os07g08940.1 | stop_gained ; p.Arg139*; HIGH | N | Average:48.667; most accessible tissue: Zhenshan97 young leaf, score: 70.177 | N | N | N | N |
| vg0704650141 | T -> A | LOC_Os07g08934.1 | upstream_gene_variant ; 3388.0bp to feature; MODIFIER | N | Average:48.667; most accessible tissue: Zhenshan97 young leaf, score: 70.177 | N | N | N | N |
| vg0704650141 | T -> A | LOC_Os07g08950.1 | upstream_gene_variant ; 2652.0bp to feature; MODIFIER | N | Average:48.667; most accessible tissue: Zhenshan97 young leaf, score: 70.177 | N | N | N | N |