21 variations found. LOC_Os02g05290 (hypothetical protein), ranging from 2,539,905 bp to 2,540,694 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Color | Explain | Details |
|---|---|---|
| red | High impact variants defined by snpEff | 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff. |
| purple | 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 | This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| vg0202539910 (J) | chr02 | 2539910 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os02g05290.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os02g05270.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g05280.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g05300.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 47.286; most accessible tissue: Minghui63 young leaf, score: 65.920 |
| vg0202539929 (J) | chr02 | 2539929 | T | C | 95.80% | 0.00% | T -> C | NA |
LOC_Os02g05290.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 46.751; most accessible tissue: Minghui63 young leaf, score: 62.741 |
| vg0202539942 (J) | chr02 | 2539942 | T | C | 95.80% | 0.00% | T -> C | NA |
LOC_Os02g05290.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 45.863; most accessible tissue: Minghui63 young leaf, score: 61.887 |
| vg0202539979 (J) | chr02 | 2539979 | G | A | 80.90% | 0.00% | A -> G |
LOC_Os02g05290.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 46.714; most accessible tissue: Minghui63 young leaf, score: 61.887 |
|
| vg0202540146 (J) | chr02 | 2540146 | A | ATTT | 95.80% | 0.00% | A -> ATTT | NA |
LOC_Os02g05270.1 Alt: ATTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: ATTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.531; most accessible tissue: Zhenshan97 panicle, score: 52.263 |
| vg0202540151 (J) | chr02 | 2540151 | G | A | 98.70% | 0.00% | G -> A | NA |
LOC_Os02g05270.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.111; most accessible tissue: Zhenshan97 panicle, score: 52.263 |
| vg0202540167 (J) | chr02 | 2540167 | T | A | 82.80% | 0.00% | T -> A | NA |
LOC_Os02g05270.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.013; most accessible tissue: Zhenshan97 panicle, score: 52.263 |
| vg0202540199 (J) | chr02 | 2540199 | C | T | 95.80% | 0.00% | C -> T | NA |
LOC_Os02g05270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 38.946; most accessible tissue: Zhenshan97 flower, score: 46.765 |
| vg0202540208 (J) | chr02 | 2540208 | A | G | 95.80% | 0.00% | A -> G | NA |
LOC_Os02g05270.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.908; most accessible tissue: Zhenshan97 flower, score: 45.926 |
| vg0202540298 (J) | chr02 | 2540298 | G | A | 81.00% | 0.00% | A -> G |
LOC_Os02g05270.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 38.724; most accessible tissue: Zhenshan97 flower, score: 47.586 |
|
| vg0202540302 (J) | chr02 | 2540302 | C | T | 93.70% | 0.00% | C -> T | NA |
LOC_Os02g05270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 38.586; most accessible tissue: Zhenshan97 flower, score: 47.586 |
| vg0202540366 (J) | chr02 | 2540366 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os02g05270.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g05280.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g05300.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g05290.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 40.879; most accessible tissue: Minghui63 panicle, score: 50.413 |
| vg0202540412 (J) | chr02 | 2540412 | A | G | 80.90% | 0.00% | G -> A |
LOC_Os02g05270.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.002; most accessible tissue: Zhenshan97 flower, score: 53.595 |
|
| vg0202540440 (J) | chr02 | 2540440 | C | T | 81.00% | 0.00% | T -> C |
LOC_Os02g05270.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.357; most accessible tissue: Minghui63 panicle, score: 71.773 |
|
| vg0202540495 (J) | chr02 | 2540495 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os02g05270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g05280.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g05300.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g05290.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.619; most accessible tissue: Minghui63 panicle, score: 73.225 |
| vg0202540545 (J) | chr02 | 2540545 | T | C | 93.50% | 0.00% | T -> C | NA |
LOC_Os02g05270.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.325; most accessible tissue: Minghui63 panicle, score: 74.563 |
| vg0202540565 (J) | chr02 | 2540565 | C | T | 80.90% | 0.00% | T -> C |
LOC_Os02g05270.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.062; most accessible tissue: Minghui63 panicle, score: 73.225 |
|
| vg0202540568 (J) | chr02 | 2540568 | T | C | 76.60% | 0.00% | C -> T | NA |
LOC_Os02g05270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05280.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05300.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g05290.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.062; most accessible tissue: Minghui63 panicle, score: 73.225 |
| vg0202540584 (J) | chr02 | 2540584 | G | A | 95.80% | 0.00% | G -> A | NA |
LOC_Os02g05290.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 56.313; most accessible tissue: Minghui63 panicle, score: 73.225 |
| vg0202540614 (J) | chr02 | 2540614 | C | T | 95.80% | 0.00% | C -> T | NA |
LOC_Os02g05290.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 57.548; most accessible tissue: Minghui63 panicle, score: 74.563 |
| vg0202540647 (J) | chr02 | 2540647 | A | G | 76.60% | 0.00% | G -> A |
LOC_Os02g05290.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 56.455; most accessible tissue: Minghui63 panicle, score: 74.563 |