Variant ID: vg1101255723 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 1255723 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 241. )
GATTACGGTACGCATCTATCTTCCTATGAAATGTTCTCTCTTGTTTTCAATAAAACTATGCTTGCACTGAATCATTTGTTTTTATAATTTTGCAGGACAA[G/A]
TTTGAAAATGAAGATCCAGATATTAAAATTGATGTATACAAAGATGAGATAATGGAACATGCCAAGTCTCTTTGGATTAACTGGCGTGGAGATTTGCATC
GATGCAAATCTCCACGCCAGTTAATCCAAAGAGACTTGGCATGTTCCATTATCTCATCTTTGTATACATCAATTTTAATATCTGGATCTTCATTTTCAAA[C/T]
TTGTCCTGCAAAATTATAAAAACAAATGATTCAGTGCAAGCATAGTTTTATTGAAAACAAGAGAGAACATTTCATAGGAAGATAGATGCGTACCGTAATC
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 | 64.50% | 4.30% | 1.78% | 29.45% | NA |
All Indica | 2759 | 51.20% | 2.40% | 1.30% | 45.13% | NA |
All Japonica | 1512 | 97.80% | 0.10% | 0.07% | 2.05% | NA |
Aus | 269 | 13.80% | 50.20% | 15.61% | 20.45% | NA |
Indica I | 595 | 20.80% | 1.70% | 2.18% | 75.29% | NA |
Indica II | 465 | 51.00% | 0.20% | 0.43% | 48.39% | NA |
Indica III | 913 | 69.20% | 3.10% | 0.88% | 26.83% | NA |
Indica Intermediate | 786 | 53.40% | 3.30% | 1.65% | 41.60% | NA |
Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
Tropical Japonica | 504 | 97.80% | 0.00% | 0.00% | 2.18% | NA |
Japonica Intermediate | 241 | 95.00% | 0.80% | 0.41% | 3.73% | NA |
VI/Aromatic | 96 | 57.30% | 1.00% | 4.17% | 37.50% | NA |
Intermediate | 90 | 70.00% | 1.10% | 1.11% | 27.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1101255723 | G -> A | LOC_Os11g03340.1 | synonymous_variant ; p.Lys188Lys; LOW | synonymous_codon | Average:6.762; most accessible tissue: Callus, score: 12.962 | N | N | N | N |
vg1101255723 | G -> DEL | LOC_Os11g03340.1 | N | frameshift_variant | Average:6.762; most accessible tissue: Callus, score: 12.962 | N | N | N | N |