| Variant ID: vg0607440894 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7440894 |
| Reference Allele: T | Alternative Allele: A,G |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTTTCTTGAAAACCCATTTGCATCCTACGGGCTTGCACCCATATGGACGCTCAACGACTTCCCAAGTACCATTAGACATAATCGAGTCCATTTCACTGCG[T/A,G]
ACTGCTTCCTTCCAATAGTCAGCGTCAGGAGATGAATATGCCTCTTCTATGGTTCTTGGGGTGTCATCCACGAGGTATACAATGTAGTCATCTCCAAAGG
CCTTTGGAGATGACTACATTGTATACCTCGTGGATGACACCCCAAGAACCATAGAAGAGGCATATTCATCTCCTGACGCTGACTATTGGAAGGAAGCAGT[A/T,C]
CGCAGTGAAATGGACTCGATTATGTCTAATGGTACTTGGGAAGTCGTTGAGCGTCCATATGGGTGCAAGCCCGTAGGATGCAAATGGGTTTTCAAGAAAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.60% | 0.10% | 9.97% | 61.36% | NA |
| All Indica | 2759 | 2.00% | 0.10% | 2.07% | 95.90% | NA |
| All Japonica | 1512 | 70.80% | 0.10% | 21.56% | 7.54% | NA |
| Aus | 269 | 67.30% | 0.00% | 2.23% | 30.48% | NA |
| Indica I | 595 | 0.50% | 0.00% | 2.69% | 96.81% | NA |
| Indica II | 465 | 1.90% | 0.20% | 1.94% | 95.91% | NA |
| Indica III | 913 | 1.30% | 0.10% | 1.42% | 97.15% | NA |
| Indica Intermediate | 786 | 3.80% | 0.00% | 2.42% | 93.77% | NA |
| Temperate Japonica | 767 | 70.40% | 0.00% | 25.16% | 4.43% | NA |
| Tropical Japonica | 504 | 72.20% | 0.20% | 16.87% | 10.71% | NA |
| Japonica Intermediate | 241 | 69.30% | 0.00% | 19.92% | 10.79% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 61.46% | 21.88% | NA |
| Intermediate | 90 | 33.30% | 0.00% | 25.56% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607440894 | T -> G | LOC_Os06g13500.1 | synonymous_variant ; p.Val775Val; LOW | N | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0607440894 | T -> A | LOC_Os06g13500.1 | synonymous_variant ; p.Val775Val; LOW | synonymous_codon | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0607440894 | T -> DEL | LOC_Os06g13500.1 | N | frameshift_variant | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |