| Variant ID: vg1007912269 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7912269 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 381. )
TGGATGAAGTCGGGGGTCGATGGACATTCTCCAGGGCAAATGAAGGCTACACGGGCTGCGGTTCGGTAGTCGAGATGTCATGGCACAGGGCCGGTGTCCT[G/A]
CTGCTAGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCCAGGATGGGTTGGAAACTAT
ATAGTTTCCAACCCATCCTGGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCTAGCAG[C/T]
AGGACACCGGCCCTGTGCCATGACATCTCGACTACCGAACCGCAGCCCGTGTAGCCTTCATTTGCCCTGGAGAATGTCCATCGACCCCCGACTTCATCCA
| 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 | 94.70% | 0.10% | 2.18% | 3.03% | NA |
| All Indica | 2759 | 92.80% | 0.10% | 3.52% | 3.62% | NA |
| All Japonica | 1512 | 97.10% | 0.00% | 0.26% | 2.65% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 81.80% | 0.00% | 10.42% | 7.73% | NA |
| Indica II | 465 | 94.60% | 0.20% | 1.94% | 3.23% | NA |
| Indica III | 913 | 98.70% | 0.00% | 0.33% | 0.99% | NA |
| Indica Intermediate | 786 | 93.10% | 0.10% | 2.93% | 3.82% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.13% | 1.17% | NA |
| Tropical Japonica | 504 | 94.60% | 0.00% | 0.60% | 4.76% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 2.22% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007912269 | G -> A | LOC_Os10g15100.1 | synonymous_variant ; p.Leu9Leu; LOW | synonymous_codon | Average:15.487; most accessible tissue: Zhenshan97 flag leaf, score: 26.688 | N | N | N | N |
| vg1007912269 | G -> DEL | LOC_Os10g15100.1 | N | frameshift_variant | Average:15.487; most accessible tissue: Zhenshan97 flag leaf, score: 26.688 | N | N | N | N |