| Variant ID: vg1007739452 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7739452 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )
CTATGAAACATATGTGATCACAATCCTTCCATTTTACTGCAGCTAGTCATTTGTTGGCACACACAATTTGAACAAAAAAATTATTACACCTCACAAAACT[G/A]
TATTTATAATTGCATGCATGTACTAAATTTCAGATAATACCAATTGTAGGCAAAATTGTTGGTTCAAAATATTTATGGTCAAGTGTACGTACCGCATTCT
AGAATGCGGTACGTACACTTGACCATAAATATTTTGAACCAACAATTTTGCCTACAATTGGTATTATCTGAAATTTAGTACATGCATGCAATTATAAATA[C/T]
AGTTTTGTGAGGTGTAATAATTTTTTTGTTCAAATTGTGTGTGCCAACAAATGACTAGCTGCAGTAAAATGGAAGGATTGTGATCACATATGTTTCATAG
| 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 | 93.70% | 0.00% | 0.17% | 6.09% | NA |
| All Indica | 2759 | 99.30% | 0.00% | 0.11% | 0.58% | NA |
| All Japonica | 1512 | 81.90% | 0.00% | 0.33% | 17.72% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.30% | 0.00% | 0.43% | 1.29% | NA |
| Indica III | 913 | 99.30% | 0.10% | 0.00% | 0.55% | NA |
| Indica Intermediate | 786 | 99.20% | 0.00% | 0.13% | 0.64% | NA |
| Temperate Japonica | 767 | 82.40% | 0.00% | 0.39% | 17.21% | NA |
| Tropical Japonica | 504 | 84.50% | 0.00% | 0.20% | 15.28% | NA |
| Japonica Intermediate | 241 | 75.10% | 0.00% | 0.41% | 24.48% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007739452 | G -> A | LOC_Os10g14280.1 | upstream_gene_variant ; 1439.0bp to feature; MODIFIER | silent_mutation | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1007739452 | G -> A | LOC_Os10g14270.1 | downstream_gene_variant ; 3395.0bp to feature; MODIFIER | silent_mutation | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1007739452 | G -> A | LOC_Os10g14295.1 | downstream_gene_variant ; 1878.0bp to feature; MODIFIER | silent_mutation | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1007739452 | G -> A | LOC_Os10g14290.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1007739452 | G -> DEL | N | N | silent_mutation | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |