| Variant ID: vg1220960435 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960435 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 304. )
TTCCAAGTGCCATACTTGTGTTCAATCGAAACAACCTCGCAAGCCTCACAAGGCATCTGAGGCGAGGAATTTGGCACCTCTAGAACTTGTTCATTCCGAT[T/C]
TGTGCGAAATGAACGGCGTGTTGACTAAAGGGGGAAAGAAATATTTCATGACACTGATAGATGATTGCACTAGATTTTGCTATGTGTATCTATTGAAAAC
GTTTTCAATAGATACACATAGCAAAATCTAGTGCAATCATCTATCAGTGTCATGAAATATTTCTTTCCCCCTTTAGTCAACACGCCGTTCATTTCGCACA[A/G]
ATCGGAATGAACAAGTTCTAGAGGTGCCAAATTCCTCGCCTCAGATGCCTTGTGAGGCTTGCGAGGTTGTTTCGATTGAACACAAGTATGGCACTTGGAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.30% | 0.10% | 2.43% | 42.11% | NA |
| All Indica | 2759 | 77.70% | 0.10% | 0.87% | 21.35% | NA |
| All Japonica | 1512 | 18.80% | 0.10% | 5.56% | 75.46% | NA |
| Aus | 269 | 50.90% | 0.40% | 1.49% | 47.21% | NA |
| Indica I | 595 | 60.70% | 0.00% | 2.02% | 37.31% | NA |
| Indica II | 465 | 77.60% | 0.00% | 0.43% | 21.94% | NA |
| Indica III | 913 | 88.20% | 0.00% | 0.11% | 11.72% | NA |
| Indica Intermediate | 786 | 78.40% | 0.40% | 1.15% | 20.10% | NA |
| Temperate Japonica | 767 | 8.70% | 0.10% | 0.65% | 90.48% | NA |
| Tropical Japonica | 504 | 33.30% | 0.00% | 9.92% | 56.75% | NA |
| Japonica Intermediate | 241 | 20.70% | 0.40% | 12.03% | 66.80% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 1.04% | 87.50% | NA |
| Intermediate | 90 | 42.20% | 1.10% | 2.22% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960435 | T -> C | LOC_Os12g34580.1 | synonymous_variant ; p.Leu607Leu; LOW | synonymous_codon | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220960435 | T -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |