Variant ID: vg0314254710 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 14254710 |
Reference Allele: C | Alternative Allele: G |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.01, others allele: 0.00, population size: 107. )
TTTTCAGAGTCAACAATTACAAGGTACTTCCTTCTTCTTACTACTTTTATTTTCTGATTCAATGCAAGAAAAACTTCATAAGTCTTCAATTTCTCGACCT[C/G]
AATCAATTGTAATCTTGTTGTCCTCTTAAGTTCAACTTGGAACTTTTTGAATATTTTTGAATTGTACAGCTTGACAGCTTGGTACTCAATGTAGTAATGA
TCATTACTACATTGAGTACCAAGCTGTCAAGCTGTACAATTCAAAAATATTCAAAAAGTTCCAAGTTGAACTTAAGAGGACAACAAGATTACAATTGATT[G/C]
AGGTCGAGAAATTGAAGACTTATGAAGTTTTTCTTGCATTGAATCAGAAAATAAAAGTAGTAAGAAGAAGGAAGTACCTTGTAATTGTTGACTCTGAAAA
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 45.50% | 38.20% | 13.73% | 2.54% | NA |
All Indica | 2759 | 70.70% | 3.20% | 21.86% | 4.20% | NA |
All Japonica | 1512 | 0.30% | 99.50% | 0.20% | 0.00% | NA |
Aus | 269 | 58.40% | 29.70% | 10.78% | 1.12% | NA |
Indica I | 595 | 62.90% | 1.30% | 33.11% | 2.69% | NA |
Indica II | 465 | 62.40% | 0.90% | 29.25% | 7.53% | NA |
Indica III | 913 | 82.90% | 4.30% | 8.98% | 3.83% | NA |
Indica Intermediate | 786 | 67.40% | 4.80% | 23.92% | 3.82% | NA |
Temperate Japonica | 767 | 0.00% | 99.90% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 0.60% | 99.20% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 0.80% | 98.80% | 0.41% | 0.00% | NA |
VI/Aromatic | 96 | 10.40% | 87.50% | 2.08% | 0.00% | NA |
Intermediate | 90 | 31.10% | 54.40% | 13.33% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0314254710 | C -> DEL | LOC_Os03g24970.1 | N | frameshift_variant | Average:6.655; most accessible tissue: Callus, score: 16.966 | N | N | N | N |
vg0314254710 | C -> G | LOC_Os03g24970.1 | missense_variant ; p.Glu59Gln; MODERATE | nonsynonymous_codon ; E59Q | Average:6.655; most accessible tissue: Callus, score: 16.966 | unknown | unknown | DELETERIOUS | 0.01 |