Search for Variation information by Variation ID:
Detailed information for vg0602928178:
| Variant ID: vg0602928178 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 2928178 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 126. )
Flanking Sequence (100 bp) in Reference Genome:
TGCCAAAATGGAGGGTGGTGATCCCCTCAAAACTTGTAGAACAGCCACTGTTGATATATATATGGTGAATAACGTAGATAATTAAATTGATGCAGGGCAA[G/A]
AGGTGATGTGCTACGAGAGCCCAAGGCCAACCATGGGGATCCACCGGCTGGTGTTCGTGCTGTTCCAGCAGCTGGGGCGTCAGACGGTGTACGCACCGGG
Reverse complement sequence
CCCGGTGCGTACACCGTCTGACGCCCCAGCTGCTGGAACAGCACGAACACCAGCCGGTGGATCCCCATGGTTGGCCTTGGGCTCTCGTAGCACATCACCT[C/T]
TTGCCCTGCATCAATTTAATTATCTACGTTATTCACCATATATATATCAACAGTGGCTGTTCTACAAGTTTTGAGGGGATCACCACCCTCCATTTTGGCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.60% | 31.50% | 1.86% | 0.00% | NA |
| All Indica | 2759 | 44.80% | 52.20% | 2.97% | 0.00% | NA |
| All Japonica | 1512 | 99.50% | 0.30% | 0.20% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 53.90% | 38.30% | 7.73% | 0.00% | NA |
| Indica II | 465 | 73.10% | 24.90% | 1.94% | 0.00% | NA |
| Indica III | 913 | 11.50% | 87.70% | 0.77% | 0.00% | NA |
| Indica Intermediate | 786 | 59.90% | 37.50% | 2.54% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.80% | 0.60% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 63.50% | 35.40% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 10.00% | 2.22% | 0.00% | NA |
QTN in RiceNavi
Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.
| Category | Variant ID | Chrom | Pos | Gene | MSU | RAP | Alt_Allele_Function | Ref_geno | Alt_geno |
|---|---|---|---|---|---|---|---|---|---|
| Heading date | vg0602928178 | Chr6 | 2928178 | RFT1 | LOC_Os06g06300 | Os06g0157500 | delaying heading date | G | A |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602928178 | G -> A | LOC_Os06g06300.1 | missense_variant ; p.Glu105Lys; MODERATE | nonsynonymous_codon ; E105K | Average:59.069; most accessible tissue: Minghui63 panicle, score: 84.552 | benign  |
0.823 |
DELETERIOUS | 0.01 |