Variant ID: vg0420972175 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 20972175 |
Reference Allele: T | Alternative Allele: A |
Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GAGAGTTTTGCATCCTAGTGAAGTGTGTACAAAGCAAGGAGCATCTCTCTCATACAGTACTGCTCAGCATGCTAGTTCAAGGTGGCTGCTGTAATTTTTG[T/A]
TCTGTCATGTGAGGTTTTATCTTACGTTCATAATGTAAAGTCCCTTTCTGAGATTGGTGAGCTGTGCAATATGTAACTTTCTTGGATTCCATCCATTACA
TGTAATGGATGGAATCCAAGAAAGTTACATATTGCACAGCTCACCAATCTCAGAAAGGGACTTTACATTATGAACGTAAGATAAAACCTCACATGACAGA[A/T]
CAAAAATTACAGCAGCCACCTTGAACTAGCATGCTGAGCAGTACTGTATGAGAGAGATGCTCCTTGCTTTGTACACACTTCACTAGGATGCAAAACTCTC
Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 57.70% | 0.30% | 2.16% | 39.86% | NA |
All Indica | 2759 | 41.20% | 0.40% | 1.88% | 56.47% | NA |
All Japonica | 1512 | 91.80% | 0.00% | 1.32% | 6.88% | NA |
Aus | 269 | 27.50% | 0.00% | 0.74% | 71.75% | NA |
Indica I | 595 | 78.70% | 0.00% | 1.01% | 20.34% | NA |
Indica II | 465 | 19.10% | 0.00% | 1.72% | 79.14% | NA |
Indica III | 913 | 35.60% | 0.80% | 1.64% | 61.99% | NA |
Indica Intermediate | 786 | 32.40% | 0.60% | 2.93% | 63.99% | NA |
Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
Tropical Japonica | 504 | 78.60% | 0.00% | 3.97% | 17.46% | NA |
Japonica Intermediate | 241 | 93.80% | 0.00% | 0.00% | 6.22% | NA |
VI/Aromatic | 96 | 62.50% | 0.00% | 27.08% | 10.42% | NA |
Intermediate | 90 | 76.70% | 0.00% | 2.22% | 21.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0420972175 | T -> DEL | N | N | silent_mutation | Average:16.058; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
vg0420972175 | T -> A | LOC_Os04g34680.1 | downstream_gene_variant ; 4188.0bp to feature; MODIFIER | silent_mutation | Average:16.058; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
vg0420972175 | T -> A | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.058; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |