| Variant ID: vg0607440891 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7440891 |
| Reference Allele: G | Alternative Allele: C,A |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCTTTTTCTTGAAAACCCATTTGCATCCTACGGGCTTGCACCCATATGGACGCTCAACGACTTCCCAAGTACCATTAGACATAATCGAGTCCATTTCACT[G/C,A]
CGTACTGCTTCCTTCCAATAGTCAGCGTCAGGAGATGAATATGCCTCTTCTATGGTTCTTGGGGTGTCATCCACGAGGTATACAATGTAGTCATCTCCAA
TTGGAGATGACTACATTGTATACCTCGTGGATGACACCCCAAGAACCATAGAAGAGGCATATTCATCTCCTGACGCTGACTATTGGAAGGAAGCAGTACG[C/G,T]
AGTGAAATGGACTCGATTATGTCTAATGGTACTTGGGAAGTCGTTGAGCGTCCATATGGGTGCAAGCCCGTAGGATGCAAATGGGTTTTCAAGAAAAAGC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.50% | 0.10% | 10.01% | 61.40% | A: 0.02% |
| All Indica | 2759 | 1.80% | 0.10% | 2.10% | 95.98% | NA |
| All Japonica | 1512 | 70.70% | 0.10% | 21.63% | 7.54% | A: 0.07% |
| Aus | 269 | 67.30% | 0.00% | 2.23% | 30.48% | NA |
| Indica I | 595 | 0.30% | 0.00% | 2.69% | 96.97% | NA |
| Indica II | 465 | 1.70% | 0.20% | 2.15% | 95.91% | NA |
| Indica III | 913 | 1.30% | 0.10% | 1.42% | 97.15% | NA |
| Indica Intermediate | 786 | 3.70% | 0.00% | 2.42% | 93.89% | NA |
| Temperate Japonica | 767 | 70.40% | 0.00% | 25.16% | 4.43% | NA |
| Tropical Japonica | 504 | 71.80% | 0.20% | 17.06% | 10.71% | A: 0.20% |
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0607440891 | G -> C | LOC_Os06g13500.1 | synonymous_variant ; p.Arg776Arg; LOW | synonymous_codon | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0607440891 | G -> A | LOC_Os06g13500.1 | synonymous_variant ; p.Arg776Arg; LOW | synonymous_codon | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0607440891 | G -> DEL | LOC_Os06g13500.1 | N | frameshift_variant | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |