| Variant ID: vg0521975611 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 21975611 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTTATTTCAGTATGTGCCGCTGGTTTTTTTTCTCTGAATTTCGCCGTGTGAACTTGAGCAATTCTAAATCATCAATTCAGGGAAATTCTTATGGACGAGC[G/A]
CAACCCTACCATGGACATAGTAGATGGTATTAGTCAATCTGTCCATGATTCACAACCGGATGGTGGTCAGTCAAGGTTGGATCGTAGCTTCCGTGAATTT
AAATTCACGGAAGCTACGATCCAACCTTGACTGACCACCATCCGGTTGTGAATCATGGACAGATTGACTAATACCATCTACTATGTCCATGGTAGGGTTG[C/T]
GCTCGTCCATAAGAATTTCCCTGAATTGATGATTTAGAATTGCTCAAGTTCACACGGCGAAATTCAGAGAAAAAAAACCAGCGGCACATACTGAAATAAA
| 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 | 37.30% | 1.00% | 7.53% | 54.17% | NA |
| All Indica | 2759 | 3.40% | 0.00% | 10.62% | 86.01% | NA |
| All Japonica | 1512 | 93.30% | 3.00% | 2.45% | 1.26% | NA |
| Aus | 269 | 45.70% | 0.00% | 6.69% | 47.58% | NA |
| Indica I | 595 | 2.40% | 0.00% | 14.62% | 83.03% | NA |
| Indica II | 465 | 3.70% | 0.00% | 8.17% | 88.17% | NA |
| Indica III | 913 | 2.20% | 0.00% | 12.05% | 85.76% | NA |
| Indica Intermediate | 786 | 5.30% | 0.00% | 7.38% | 87.28% | NA |
| Temperate Japonica | 767 | 90.40% | 4.60% | 3.78% | 1.30% | NA |
| Tropical Japonica | 504 | 98.20% | 0.20% | 0.60% | 0.99% | NA |
| Japonica Intermediate | 241 | 92.10% | 4.10% | 2.07% | 1.66% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 8.89% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0521975611 | G -> DEL | LOC_Os05g37540.1 | N | frameshift_variant | Average:4.456; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0521975611 | G -> A | LOC_Os05g37540.1 | missense_variant ; p.Arg25His; MODERATE | nonsynonymous_codon ; R25H | Average:4.456; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.59 |