| Variant ID: vg0607440927 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7440927 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 236. )
TGCACCCATATGGACGCTCAACGACTTCCCAAGTACCATTAGACATAATCGAGTCCATTTCACTGCGTACTGCTTCCTTCCAATAGTCAGCGTCAGGAGA[T/G]
GAATATGCCTCTTCTATGGTTCTTGGGGTGTCATCCACGAGGTATACAATGTAGTCATCTCCAAAGGATTTTGCAACCCTTTGTCTCTTACTCTTGCGAG
CTCGCAAGAGTAAGAGACAAAGGGTTGCAAAATCCTTTGGAGATGACTACATTGTATACCTCGTGGATGACACCCCAAGAACCATAGAAGAGGCATATTC[A/C]
TCTCCTGACGCTGACTATTGGAAGGAAGCAGTACGCAGTGAAATGGACTCGATTATGTCTAATGGTACTTGGGAAGTCGTTGAGCGTCCATATGGGTGCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 6.50% | 0.10% | 6.81% | 86.56% | NA |
| All Indica | 2759 | 0.70% | 0.00% | 1.78% | 97.54% | NA |
| All Japonica | 1512 | 15.00% | 0.30% | 12.30% | 72.42% | NA |
| Aus | 269 | 20.80% | 0.00% | 5.58% | 73.61% | NA |
| Indica I | 595 | 0.20% | 0.00% | 1.85% | 97.98% | NA |
| Indica II | 465 | 0.40% | 0.20% | 1.94% | 97.42% | NA |
| Indica III | 913 | 0.20% | 0.00% | 1.20% | 98.58% | NA |
| Indica Intermediate | 786 | 1.70% | 0.00% | 2.29% | 96.06% | NA |
| Temperate Japonica | 767 | 15.60% | 0.40% | 11.34% | 72.62% | NA |
| Tropical Japonica | 504 | 14.70% | 0.20% | 15.08% | 70.04% | NA |
| Japonica Intermediate | 241 | 13.70% | 0.00% | 9.54% | 76.76% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 63.54% | 35.42% | NA |
| Intermediate | 90 | 6.70% | 0.00% | 12.22% | 81.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607440927 | T -> G | LOC_Os06g13500.1 | synonymous_variant ; p.Ser764Ser; LOW | synonymous_codon | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0607440927 | T -> DEL | LOC_Os06g13500.1 | N | frameshift_variant | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |