Search for Variation information by Variation ID:
Detailed information for vg0620602800:
| Variant ID: vg0620602800 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602800 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.25, others allele: 0.00, population size: 213. )
Flanking Sequence (100 bp) in Reference Genome:
AAAGCAATGGTACACCTCTACTGTTGGATGTGTAAGCGGTAGTTGGGAGAAGTTGCGAGACAGATTCTGTCTTTCCTTCTTCCCAGTTACTCGTATTACT[G/A]
CCCTTCGAGTAGAAATTCTCAGTTTCAATCGGTGCAGCCTGTCCAGATTCACTAATTTAGTGCAGTCCGGACCAACCCTATCCTTACCCGAATATGTGCT
Reverse complement sequence
AGCACATATTCGGGTAAGGATAGGGTTGGTCCGGACTGCACTAAATTAGTGAATCTGGACAGGCTGCACCGATTGAAACTGAGAATTTCTACTCGAAGGG[C/T]
AGTAATACGAGTAACTGGGAAGAAGGAAAGACAGAATCTGTCTCGCAACTTCTCCCAACTACCGCTTACACATCCAACAGTAGAGGTGTACCATTGCTTT
Allele Frequencies:
| 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 | 66.10% | 32.50% | 0.13% | 1.25% | NA |
| All Indica | 2759 | 98.00% | 1.80% | 0.07% | 0.07% | NA |
| All Japonica | 1512 | 4.10% | 92.10% | 0.13% | 3.64% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.10% | 0.80% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 96.70% | 2.90% | 0.25% | 0.13% | NA |
| Temperate Japonica | 767 | 2.90% | 96.30% | 0.13% | 0.65% | NA |
| Tropical Japonica | 504 | 7.10% | 91.50% | 0.00% | 1.39% | NA |
| Japonica Intermediate | 241 | 1.70% | 80.10% | 0.41% | 17.84% | NA |
| VI/Aromatic | 96 | 46.90% | 53.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 51.10% | 44.40% | 2.22% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602800 | G -> A | LOC_Os06g35340.1 | missense_variant ; p.Ala82Thr; MODERATE | nonsynonymous_codon ; A82T | Average:18.528; most accessible tissue: Zhenshan97 root, score: 25.639 | benign  |
0.118 |
TOLERATED | 1.00 |
| vg0620602800 | G -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:18.528; most accessible tissue: Zhenshan97 root, score: 25.639 | N | N | N | N |