| Variant ID: vg0710351290 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10351290 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTCGGAAAGTAAACGTCGCAATGCTCGACCAATATCCACAAGAAACAGAGGACAATCTCGTCCATCTCCTGAAGGCGCAGCATTACAAGACGTTCATACT[G/A]
TTGCCATACAACACAGAGTTAGTTTAATTTTACTGTCTTCCTACATACCAAATTTCATTCCCGTACGAACTTGCTAAGTGTTTCATATGTAATGCATCCC
GGGATGCATTACATATGAAACACTTAGCAAGTTCGTACGGGAATGAAATTTGGTATGTAGGAAGACAGTAAAATTAAACTAACTCTGTGTTGTATGGCAA[C/T]
AGTATGAACGTCTTGTAATGCTGCGCCTTCAGGAGATGGACGAGATTGTCCTCTGTTTCTTGTGGATATTGGTCGAGCATTGCGACGTTTACTTTCCGAG
| 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 | 30.40% | 0.10% | 5.08% | 64.35% | NA |
| All Indica | 2759 | 5.30% | 0.00% | 3.37% | 91.34% | NA |
| All Japonica | 1512 | 73.70% | 0.50% | 9.39% | 16.40% | NA |
| Aus | 269 | 50.90% | 0.00% | 1.12% | 47.96% | NA |
| Indica I | 595 | 8.40% | 0.00% | 0.84% | 90.76% | NA |
| Indica II | 465 | 6.20% | 0.00% | 1.51% | 92.26% | NA |
| Indica III | 913 | 1.50% | 0.00% | 2.52% | 95.95% | NA |
| Indica Intermediate | 786 | 6.70% | 0.00% | 7.38% | 85.88% | NA |
| Temperate Japonica | 767 | 61.50% | 0.00% | 14.47% | 23.99% | NA |
| Tropical Japonica | 504 | 89.30% | 0.20% | 0.20% | 10.32% | NA |
| Japonica Intermediate | 241 | 80.10% | 2.50% | 12.45% | 4.98% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 2.08% | 95.83% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 0.00% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710351290 | G -> DEL | LOC_Os07g17510.1 | N | frameshift_variant | Average:5.041; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0710351290 | G -> A | LOC_Os07g17510.1 | synonymous_variant ; p.Leu851Leu; LOW | synonymous_codon | Average:5.041; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |