7 variations found. LOC_Os04g45060 (MYB family transcription factor; putative; expressed), ranging from 26,660,001 bp to 26,661,400 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0426660213 (J) | chr04 | 26660213 | G | GT | 95.50% | 0.00% | G -> GT | NA |
LOC_Os04g45050.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45070.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45060.1 Alt: GT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.178; most accessible tissue: Zhenshan97 flower, score: 93.634 |
| vg0426660345 (J) | chr04 | 26660345 | G | A | 95.50% | 0.00% | G -> A | NA |
LOC_Os04g45060.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.990; most accessible tissue: Zhenshan97 flower, score: 93.469 |
| vg0426660506 (J) | chr04 | 26660506 | C | T | 95.50% | 0.00% | C -> T | NA |
LOC_Os04g45050.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45060.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.268; most accessible tissue: Callus, score: 91.642 |
| vg0426660821 (J) | chr04 | 26660821 | T | C | 95.50% | 0.00% | T -> C | NA |
LOC_Os04g45060.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.774; most accessible tissue: Zhenshan97 root, score: 89.783 |
| vg0426660905 (J) | chr04 | 26660905 | C | A | 80.10% | 2.16% | C -> A | NA |
LOC_Os04g45060.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g45060.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 83.442; most accessible tissue: Zhenshan97 panicle, score: 89.143 |
| vg0426660980 (J) | chr04 | 26660980 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os04g45060.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 83.011; most accessible tissue: Zhenshan97 panicle, score: 88.625 |
| STR0426660214 (J) | chr04 | 26660214 | TT | TTT | 97.90% | 0.00% | TT -> TTT | NA |
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