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Detailed information for vg0728251061:
| Variant ID: vg0728251061 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 28251061 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 340. )
Flanking Sequence (100 bp) in Reference Genome:
CGCAATGAGGGGTCGAGATGTTGCATTCTCCTGCAAGCACATAGATGCAACAGCTAAAGCCTGGTACAAACCCCTTTTGGGATAACAACCTTGCAGCGAT[G/T]
GATCGGCCATTTGGCAGAACTTCCTTCGGTCTCTAAACAGTGGACGAGCCTGCAAATTATAAGGATAAGACACTTCACATCATGATGAAATTGAAACAGA
Reverse complement sequence
TCTGTTTCAATTTCATCATGATGTGAAGTGTCTTATCCTTATAATTTGCAGGCTCGTCCACTGTTTAGAGACCGAAGGAAGTTCTGCCAAATGGCCGATC[C/A]
ATCGCTGCAAGGTTGTTATCCCAAAAGGGGTTTGTACCAGGCTTTAGCTGTTGCATCTATGTGCTTGCAGGAGAATGCAACATCTCGACCCCTCATTGCG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.90% | 1.00% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 98.30% | 1.60% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.70% | 4.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.60% | 0.13% | 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 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0728251061 | G -> T | LOC_Os07g47270.1 | missense_variant ; p.Pro313Gln; MODERATE | nonsynonymous_codon ; P313Q | Average:59.502; most accessible tissue: Callus, score: 83.022 | probably damaging  |
2.8 |
DELETERIOUS | 0.00 |