| Variant ID: vg1007738360 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7738360 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )
CCCATCACAACTCAAAGTAAAGTACAGTGCACAAACTACCAGGTGCCACCAGATGACTGTCCAGTACCACCAGTGCGTATAAATTCCAAGCGCCTAGCGG[C/A]
GTCCTTGAGTCGAACAAAGCATTTGCAGGTGAATGGGTCACGGAATAGCGCACAAGCAGCATACCACACACTTCCTCCAATTTCATGGCCATCATTTTCC
GGAAAATGATGGCCATGAAATTGGAGGAAGTGTGTGGTATGCTGCTTGTGCGCTATTCCGTGACCCATTCACCTGCAAATGCTTTGTTCGACTCAAGGAC[G/T]
CCGCTAGGCGCTTGGAATTTATACGCACTGGTGGTACTGGACAGTCATCTGGTGGCACCTGGTAGTTTGTGCACTGTACTTTACTTTGAGTTGTGATGGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.20% | 0.00% | 2.43% | 10.37% | NA |
| All Indica | 2759 | 89.70% | 0.00% | 2.21% | 8.05% | NA |
| All Japonica | 1512 | 79.90% | 0.00% | 2.84% | 17.26% | NA |
| Aus | 269 | 97.80% | 0.00% | 1.86% | 0.37% | NA |
| Indica I | 595 | 79.20% | 0.00% | 4.03% | 16.81% | NA |
| Indica II | 465 | 91.20% | 0.00% | 2.80% | 6.02% | NA |
| Indica III | 913 | 96.90% | 0.00% | 0.33% | 2.74% | NA |
| Indica Intermediate | 786 | 88.50% | 0.00% | 2.67% | 8.78% | NA |
| Temperate Japonica | 767 | 81.70% | 0.00% | 2.35% | 15.91% | NA |
| Tropical Japonica | 504 | 80.00% | 0.00% | 4.37% | 15.67% | NA |
| Japonica Intermediate | 241 | 73.90% | 0.00% | 1.24% | 24.90% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 5.21% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 1.11% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738360 | C -> A | LOC_Os10g14290.1 | missense_variant ; p.Ala384Ser; MODERATE | N | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |
| vg1007738360 | C -> A | LOC_Os10g14260.1 | upstream_gene_variant ; 4109.0bp to feature; MODIFIER | N | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |
| vg1007738360 | C -> A | LOC_Os10g14280.1 | upstream_gene_variant ; 347.0bp to feature; MODIFIER | N | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |
| vg1007738360 | C -> A | LOC_Os10g14270.1 | downstream_gene_variant ; 2303.0bp to feature; MODIFIER | N | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |
| vg1007738360 | C -> A | LOC_Os10g14295.1 | downstream_gene_variant ; 2970.0bp to feature; MODIFIER | N | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |