9 variations found. LOC_Os04g41060 (zinc finger C-x8-C-x5-C-x3-H type family protein; expressed), ranging from 24,359,393 bp to 24,360,538 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0424359435 (J) | chr04 | 24359435 | C | A | 73.30% | 0.00% | C -> A | NA |
LOC_Os04g41060.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.067; most accessible tissue: Zhenshan97 flower, score: 92.566 |
| vg0424359618 (J) | chr04 | 24359618 | G | T | 98.30% | 0.00% | G -> T | NA |
LOC_Os04g41040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41050.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41040.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41060.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.038; most accessible tissue: Zhenshan97 flower, score: 91.937 |
| vg0424359788 (J) | chr04 | 24359788 | C | CT | 99.20% | 0.00% | C -> CT | NA |
LOC_Os04g41040.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41050.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41040.2 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41070.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41060.1 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.832; most accessible tissue: Minghui63 flower, score: 88.094 |
| vg0424359848 (J) | chr04 | 24359848 | T | TTA | 98.60% | 0.00% | T -> TTA | NA |
LOC_Os04g41040.1 Alt: TTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41050.1 Alt: TTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41040.2 Alt: TTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41070.1 Alt: TTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41060.1 Alt: TTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.721; most accessible tissue: Minghui63 flower, score: 87.676 |
| vg0424360064 (J) | chr04 | 24360064 | GT | GTT | 97.30% | 0.00% | GT -> GTT,G,GTTT | NA |
LOC_Os04g41040.1 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41050.1 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41040.2 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41070.1 Alt: GTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41060.1 Alt: GTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41050.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41040.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41070.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41060.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41040.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41050.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41040.2 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41070.1 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41060.1 Alt: GTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.762; most accessible tissue: Minghui63 flower, score: 93.446 |
| vg0424360155 (J) | chr04 | 24360155 | C | T | 73.30% | 0.06% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41050.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41040.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41060.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 90.082; most accessible tissue: Minghui63 flower, score: 95.787 |
| vg0424360285 (J) | chr04 | 24360285 | G | T | 73.20% | 0.00% | G -> T | NA |
LOC_Os04g41040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41050.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41040.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41060.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.247; most accessible tissue: Minghui63 flower, score: 97.259 |
| vg0424360477 (J) | chr04 | 24360477 | A | ACGGCGA GT | 98.30% | 0.00% | A -> ACGGCGAGT | NA |
LOC_Os04g41060.1 Alt: ACGGCGAGT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.741; most accessible tissue: Zhenshan97 panicle, score: 97.682 |
| STR0424359433 (J) | chr04 | 24359433 | TCC | TCA | 83.60% | 0.00% | TCC -> TCA | NA |
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