Variant ID: vg0327370221 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 27370221 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.28, others allele: 0.00, population size: 191. )
AACTCTCAATCCGCTTTTTTATCTCTTCGATAATTAACGGGAAATCCCGCCTAAGATGAAAGTAGCCATCAGTGACGGCCACCTTCTTGAAGTTGATCTC[C/T]
GCCATCAAGAAGCTGAGCCACTTGCTCTTTAGCTCCGGGCAATGGTACCTCTCGGCGTAGGCGCGTAGCCTAGAGTCATCGCCACCGTCTCCACCGACAC
GTGTCGGTGGAGACGGTGGCGATGACTCTAGGCTACGCGCCTACGCCGAGAGGTACCATTGCCCGGAGCTAAAGAGCAAGTGGCTCAGCTTCTTGATGGC[G/A]
GAGATCAACTTCAAGAAGGTGGCCGTCACTGATGGCTACTTTCATCTTAGGCGGGATTTCCCGTTAATTATCGAAGAGATAAAAAAGCGGATTGAGAGTT
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 64.40% | 35.30% | 0.02% | 0.23% | NA |
All Indica | 2759 | 97.80% | 1.90% | 0.04% | 0.25% | NA |
All Japonica | 1512 | 1.20% | 98.60% | 0.00% | 0.20% | NA |
Aus | 269 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.00% | 0.80% | 0.00% | 0.17% | NA |
Indica II | 465 | 98.30% | 1.10% | 0.00% | 0.65% | NA |
Indica III | 913 | 97.20% | 2.60% | 0.11% | 0.11% | NA |
Indica Intermediate | 786 | 97.30% | 2.40% | 0.00% | 0.25% | NA |
Temperate Japonica | 767 | 0.50% | 99.20% | 0.00% | 0.26% | NA |
Tropical Japonica | 504 | 1.80% | 98.00% | 0.00% | 0.20% | NA |
Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 16.70% | 83.30% | 0.00% | 0.00% | NA |
Intermediate | 90 | 57.80% | 41.10% | 0.00% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0327370221 | C -> T | LOC_Os03g48120.1 | synonymous_variant ; p.Ala170Ala; LOW | synonymous_codon | Average:77.274; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
vg0327370221 | C -> DEL | LOC_Os03g48120.1 | N | frameshift_variant | Average:77.274; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |