Variant ID: vg0409515128 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 9515128 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGGCCATCTCAAGACGATGTAAAACACATCGGCTGTCATGCATCAGCAACACTAGCCGATCATGCGTCAACCCAAACACTTGGGTAATACTTCTTCAAGT[A/G]
TTTGCCATTGAGCGCCCATCCATAAACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACATTATAGATTTGAAACGGTCCTTCCCAA
TTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTTTATGGATGGGCGCTCAATGGCAAA[T/C]
ACTTGAAGAAGTATTACCCAAGTGTTTGGGTTGACGCATGATCGGCTAGTGTTGCTGATGCATGACAGCCGATGTGTTTTACATCGTCTTGAGATGGCCG
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 91.10% | 0.10% | 0.83% | 8.00% | NA |
All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 74.10% | 0.10% | 2.12% | 23.74% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
Tropical Japonica | 504 | 33.70% | 0.00% | 5.36% | 60.91% | NA |
Japonica Intermediate | 241 | 80.50% | 0.40% | 2.07% | 17.01% | NA |
VI/Aromatic | 96 | 75.00% | 1.00% | 5.21% | 18.75% | NA |
Intermediate | 90 | 97.80% | 0.00% | 1.11% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0409515128 | A -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:37.548; most accessible tissue: Minghui63 young leaf, score: 63.571 | N | N | N | N |
vg0409515128 | A -> G | LOC_Os04g17380.1 | missense_variant ; p.Tyr160His; MODERATE | nonsynonymous_codon ; Y160H | Average:37.548; most accessible tissue: Minghui63 young leaf, score: 63.571 | probably damaging | 2.485 | TOLERATED | 0.09 |