Variant ID: vg0500376864 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 376864 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 354. )
TATCCGCTCCCCCAGTTCCCACTCCCCTCGGAACCGGCACAACCCAAGCAAACCACCCAATGCATGTGCCTTCAACTCCTCTGGCATACTCGTTAAGAGA[C/T]
CCTCAGCTTCTTCCAGAAGCCCAACACTTGCATACAGATTGGCCATGCACCAATAATGTGCAAATGTTGGCTTGATGTTGTACATGGTGCTCATCTGCTC
GAGCAGATGAGCACCATGTACAACATCAAGCCAACATTTGCACATTATTGGTGCATGGCCAATCTGTATGCAAGTGTTGGGCTTCTGGAAGAAGCTGAGG[G/A]
TCTCTTAACGAGTATGCCAGAGGAGTTGAAGGCACATGCATTGGGTGGTTTGCTTGGGTTGTGCCGGTTCCGAGGGGAGTGGGAACTGGGGGAGCGGATA
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
All Indica | 2759 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0500376864 | C -> T | LOC_Os05g01635.1 | missense_variant ; p.Gly423Asp; MODERATE | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0500376864 | C -> T | LOC_Os05g01630.1 | upstream_gene_variant ; 1181.0bp to feature; MODIFIER | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0500376864 | C -> T | LOC_Os05g01640.1 | upstream_gene_variant ; 4310.0bp to feature; MODIFIER | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0500376864 | C -> T | LOC_Os05g01630.2 | upstream_gene_variant ; 1181.0bp to feature; MODIFIER | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0500376864 | C -> T | LOC_Os05g01630.3 | upstream_gene_variant ; 1181.0bp to feature; MODIFIER | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |