Variant ID: vg1212666270 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 12666270 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )
AGCTGGTTGACAAAGCAATTCGCCTTGAAGACAAGAAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCA[G/A]
AGGCAGCGTATCAAGCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTA
TAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGCTTGATACGCTGCCT[C/T]
TGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTTCTTGTCTTCAAGGCGAATTGCTTTGTCAACCAGCT
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 79.50% | 0.10% | 1.52% | 18.90% | NA |
All Indica | 2759 | 83.30% | 0.00% | 1.27% | 15.40% | NA |
All Japonica | 1512 | 69.80% | 0.10% | 1.85% | 28.31% | NA |
Aus | 269 | 94.10% | 0.40% | 0.37% | 5.20% | NA |
Indica I | 595 | 70.60% | 0.00% | 2.02% | 27.39% | NA |
Indica II | 465 | 83.40% | 0.00% | 1.29% | 15.27% | NA |
Indica III | 913 | 91.50% | 0.00% | 0.55% | 8.00% | NA |
Indica Intermediate | 786 | 83.50% | 0.00% | 1.53% | 15.01% | NA |
Temperate Japonica | 767 | 83.60% | 0.00% | 0.13% | 16.30% | NA |
Tropical Japonica | 504 | 57.70% | 0.00% | 3.57% | 38.69% | NA |
Japonica Intermediate | 241 | 51.00% | 0.40% | 3.73% | 44.81% | NA |
VI/Aromatic | 96 | 82.30% | 4.20% | 3.12% | 10.42% | NA |
Intermediate | 90 | 76.70% | 0.00% | 5.56% | 17.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1212666270 | G -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg1212666270 | G -> A | LOC_Os12g22430.1 | synonymous_variant ; p.Gln245Gln; LOW | synonymous_codon | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |