| Variant ID: vg0625222860 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 25222860 |
| Reference Allele: A | Alternative Allele: ACGACGCCTTGGC |
| Primary Allele: A | Secondary Allele: ACGACGCCTTGGC |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 94. )
ATATTATGCAAGATAAATGACATAATTGTTGGAAGTAATACAAATTGGACGTACCGCCACGAAGTAGTCTCGGTCACGGTGCGTGGGATACGCGTCCGTG[A/ACGACGCCTTGGC]
CAGCGGCAACGTGCGGCTCTGGGGCGTCTGGAGTGAAGGTCACACGCGCACGAGTGCGAGGAAGGTACCAGCGAAGGTCACACTTGCTGCAGCGTAAAGT
ACTTTACGCTGCAGCAAGTGTGACCTTCGCTGGTACCTTCCTCGCACTCGTGCGCGTGTGACCTTCACTCCAGACGCCCCAGAGCCGCACGTTGCCGCTG[T/GCCAAGGCGTCGT]
CACGGACGCGTATCCCACGCACCGTGACCGAGACTACTTCGTGGCGGTACGTCCAATTTGTATTACTTCCAACAATTATGTCATTTATCTTGCATAATAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of ACGACGCCTTGGC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 15.50% | 0.20% | 3.26% | 81.06% | NA |
| All Indica | 2759 | 0.70% | 0.10% | 2.39% | 96.81% | NA |
| All Japonica | 1512 | 45.80% | 0.00% | 0.60% | 53.57% | NA |
| Aus | 269 | 1.90% | 0.00% | 17.84% | 80.30% | NA |
| Indica I | 595 | 0.70% | 0.00% | 1.01% | 98.32% | NA |
| Indica II | 465 | 1.10% | 0.00% | 2.37% | 96.56% | NA |
| Indica III | 913 | 0.50% | 0.10% | 3.07% | 96.28% | NA |
| Indica Intermediate | 786 | 0.60% | 0.30% | 2.67% | 96.44% | NA |
| Temperate Japonica | 767 | 72.50% | 0.00% | 0.26% | 27.25% | NA |
| Tropical Japonica | 504 | 8.10% | 0.00% | 0.79% | 91.07% | NA |
| Japonica Intermediate | 241 | 39.80% | 0.00% | 1.24% | 58.92% | NA |
| VI/Aromatic | 96 | 7.30% | 4.20% | 28.12% | 60.42% | NA |
| Intermediate | 90 | 10.00% | 1.10% | 4.44% | 84.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625222860 | A -> ACGACGCCTTGGC | LOC_Os06g42010.1 | inframe_insertion ; p.Ala762_Val763insGlyGlnGlyVal; MODERATE | inframe_variant | Average:4.868; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0625222860 | A -> DEL | LOC_Os06g42010.1 | N | frameshift_variant | Average:4.868; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |