Variant ID: vg0804463753 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 4463753 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GAAAACCGGTCGGCTTTGGCGAAATTCCGAGCGAAATCATCGAAATTTCAATCAATAACTATAAATAGAGGTAAACTAAAATTGTTTTCCTTTTTTAATT[C/A]
GTTATTCTTTTCTTTCCTATTGTAAATTTCAGTAAATACATGGAATACATCAGTTTTTTTGAAAATTTATATCCCAATAGGTTCTATGAATATCATACTA
TAGTATGATATTCATAGAACCTATTGGGATATAAATTTTCAAAAAAACTGATGTATTCCATGTATTTACTGAAATTTACAATAGGAAAGAAAAGAATAAC[G/T]
AATTAAAAAAGGAAAACAATTTTAGTTTACCTCTATTTATAGTTATTGATTGAAATTTCGATGATTTCGCTCGGAATTTCGCCAAAGCCGACCGGTTTTC
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 36.00% | 0.10% | 1.27% | 62.63% | NA |
All Indica | 2759 | 6.20% | 0.10% | 1.45% | 92.32% | NA |
All Japonica | 1512 | 95.20% | 0.10% | 0.07% | 4.70% | NA |
Aus | 269 | 11.20% | 0.00% | 4.83% | 84.01% | NA |
Indica I | 595 | 9.60% | 0.00% | 1.34% | 89.08% | NA |
Indica II | 465 | 7.70% | 0.00% | 2.58% | 89.68% | NA |
Indica III | 913 | 2.30% | 0.00% | 0.77% | 96.93% | NA |
Indica Intermediate | 786 | 7.10% | 0.30% | 1.65% | 90.97% | NA |
Temperate Japonica | 767 | 98.30% | 0.00% | 0.13% | 1.56% | NA |
Tropical Japonica | 504 | 89.30% | 0.00% | 0.00% | 10.71% | NA |
Japonica Intermediate | 241 | 97.50% | 0.40% | 0.00% | 2.07% | NA |
VI/Aromatic | 96 | 22.90% | 3.10% | 3.12% | 70.83% | NA |
Intermediate | 90 | 43.30% | 0.00% | 3.33% | 53.33% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0804463753 | C -> A | LOC_Os08g07900.1 | upstream_gene_variant ; 3530.0bp to feature; MODIFIER | silent_mutation | Average:15.069; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
vg0804463753 | C -> A | LOC_Os08g07910.1 | upstream_gene_variant ; 2632.0bp to feature; MODIFIER | silent_mutation | Average:15.069; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
vg0804463753 | C -> A | LOC_Os08g07930.1 | upstream_gene_variant ; 2276.0bp to feature; MODIFIER | silent_mutation | Average:15.069; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
vg0804463753 | C -> A | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.069; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
vg0804463753 | C -> DEL | N | N | silent_mutation | Average:15.069; most accessible tissue: Callus, score: 29.336 | N | N | N | N |