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Detailed information for vg0704593747:
| Variant ID: vg0704593747 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4593747 |
| 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: 368. )
Flanking Sequence (100 bp) in Reference Genome:
CAACTCTGGTGCAGGTAGCACAATCCTCTAGCAACTCCTATAGCTATTTGATACCTGGTGCTCCAATTTAGAACGGTAGCATTGCTCTGAAATAGATGGG[C/T]
GTCAAGAGACCCATTTAACATGCGTTCATACACAAGTAGCCTCTTATCACCTTCGCAGCAGAAACCAATCAGTTTGATTAGGTTGATATGTTGGGTCATT
Reverse complement sequence
AATGACCCAACATATCAACCTAATCAAACTGATTGGTTTCTGCTGCGAAGGTGATAAGAGGCTACTTGTGTATGAACGCATGTTAAATGGGTCTCTTGAC[G/A]
CCCATCTATTTCAGAGCAATGCTACCGTTCTAAATTGGAGCACCAGGTATCAAATAGCTATAGGAGTTGCTAGAGGATTGTGCTACCTGCACCAGAGTTG
Allele Frequencies:
| 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 | 99.70% | 0.30% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 94.80% | 4.50% | 0.74% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 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 |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0704593747 | C -> T | LOC_Os07g08860.1 | missense_variant ; p.Ala621Thr; MODERATE | nonsynonymous_codon ; A621T | Average:56.741; most accessible tissue: Zhenshan97 panicle, score: 68.538 | benign  |
0.594 |
TOLERATED | 0.51 |