| Variant ID: vg1007738361 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7738361 |
| 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: 322. )
CCATCACAACTCAAAGTAAAGTACAGTGCACAAACTACCAGGTGCCACCAGATGACTGTCCAGTACCACCAGTGCGTATAAATTCCAAGCGCCTAGCGGC[G/A]
TCCTTGAGTCGAACAAAGCATTTGCAGGTGAATGGGTCACGGAATAGCGCACAAGCAGCATACCACACACTTCCTCCAATTTCATGGCCATCATTTTCCA
TGGAAAATGATGGCCATGAAATTGGAGGAAGTGTGTGGTATGCTGCTTGTGCGCTATTCCGTGACCCATTCACCTGCAAATGCTTTGTTCGACTCAAGGA[C/T]
GCCGCTAGGCGCTTGGAATTTATACGCACTGGTGGTACTGGACAGTCATCTGGTGGCACCTGGTAGTTTGTGCACTGTACTTTACTTTGAGTTGTGATGG
| 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 | 87.30% | 0.20% | 2.24% | 10.30% | NA |
| All Indica | 2759 | 89.50% | 0.30% | 2.17% | 8.05% | NA |
| All Japonica | 1512 | 80.10% | 0.10% | 2.71% | 17.13% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 79.30% | 0.00% | 3.87% | 16.81% | NA |
| Indica II | 465 | 90.50% | 0.00% | 3.44% | 6.02% | NA |
| Indica III | 913 | 96.20% | 0.50% | 0.55% | 2.74% | NA |
| Indica Intermediate | 786 | 88.90% | 0.30% | 2.04% | 8.78% | NA |
| Temperate Japonica | 767 | 81.60% | 0.00% | 2.48% | 15.91% | NA |
| Tropical Japonica | 504 | 80.80% | 0.20% | 3.77% | 15.28% | 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 | 93.30% | 0.00% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738361 | G -> A | LOC_Os10g14290.1 | synonymous_variant ; p.Asp383Asp; LOW | synonymous_codon | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |
| vg1007738361 | G -> DEL | LOC_Os10g14290.1 | N | frameshift_variant | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |