63 variations found. LOC_Os04g52074 (expressed protein), ranging from 30,927,630 bp to 30,934,100 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0430929477 (J) | chr04 | 30929477 | T | G | 93.00% | 0.00% | T -> G | NA |
|
| STR0430931990 (J) | chr04 | 30931990 | GCTTGAG C | GCTTGAG T | 96.10% | 0.00% | GCTTGAGC -> GCTTGAGT | NA |
|
| vg0430927640 (J) | chr04 | 30927640 | G | GA | 96.90% | 0.00% | G -> GA | NA |
LOC_Os04g52074.1 Alt: GA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g52060.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.287; most accessible tissue: Zhenshan97 flag leaf, score: 98.172 |
| vg0430927651 (J) | chr04 | 30927651 | GA | GAA | 94.80% | 0.00% | GA -> GAA,AA,G | NA |
LOC_Os04g52074.1 Alt: GAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g52060.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g52074.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g52060.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g52074.1 Alt: AA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g52060.1 Alt: AA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.441; most accessible tissue: Zhenshan97 flag leaf, score: 98.320 |
| vg0430927655 (J) | chr04 | 30927655 | A | G | 99.40% | 0.00% | A -> G | NA |
LOC_Os04g52074.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g52060.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.559; most accessible tissue: Zhenshan97 flag leaf, score: 98.372 |
| vg0430927673 (J) | chr04 | 30927673 | G | A | 96.40% | 0.00% | G -> A |
LOC_Os04g52074.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g52060.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.699; most accessible tissue: Zhenshan97 flag leaf, score: 98.424 |
|
| vg0430927712 (J) | chr04 | 30927712 | C | T | 95.40% | 0.00% | C -> T | NA |
LOC_Os04g52074.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 96.535; most accessible tissue: Zhenshan97 flag leaf, score: 98.348 |
| vg0430927890 (J) | chr04 | 30927890 | C | T | 67.90% | 6.64% | C -> T | NA |
LOC_Os04g52074.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g52074.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 90.246; most accessible tissue: Zhenshan97 flag leaf, score: 97.657 |
| vg0430927909 (J) | chr04 | 30927909 | C | G | 98.90% | 0.00% | C -> G | NA |
LOC_Os04g52074.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.114; most accessible tissue: Zhenshan97 flag leaf, score: 97.589 |
| vg0430928658 (J) | chr04 | 30928658 | T | C | 85.90% | 0.00% | T -> C | NA |
LOC_Os04g52060.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g52074.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.554; most accessible tissue: Minghui63 flower, score: 60.681 |
| vg0430928869 (J) | chr04 | 30928869 | T | C | 94.10% | 0.00% | T -> C | NA |
LOC_Os04g52060.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g52074.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.872; most accessible tissue: Minghui63 flower, score: 55.046 |
| vg0430929112 (J) | chr04 | 30929112 | G | A | 94.10% | 0.00% | G -> A | NA |
LOC_Os04g52060.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g52074.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.474; most accessible tissue: Callus, score: 61.917 |
| vg0430929152 (J) | chr04 | 30929152 | A | G | 95.40% | 0.00% | A -> G | NA |
LOC_Os04g52060.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g52074.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.587; most accessible tissue: Callus, score: 61.917 |
| vg0430929263 (J) | chr04 | 30929263 | G | A | 96.90% | 0.00% | G -> A | NA |
LOC_Os04g52074.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 50.022; most accessible tissue: Callus, score: 87.307 |
| vg0430929291 (J) | chr04 | 30929291 | T | C | 86.00% | 0.00% | T -> C | NA |
LOC_Os04g52074.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 50.373; most accessible tissue: Callus, score: 87.307 |
| vg0430929455 (J) | chr04 | 30929455 | C | A | 91.90% | 0.00% | C -> A | NA |
LOC_Os04g52074.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 62.963; most accessible tissue: Callus, score: 88.852 |
| vg0430929477 (J) | chr04 | 30929477 | T | G | 85.90% | 0.00% | T -> G | NA |
LOC_Os04g52074.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 64.287; most accessible tissue: Callus, score: 88.852 |
| vg0430929673 (J) | chr04 | 30929673 | C | A | 99.60% | 0.00% | C -> A | NA |
LOC_Os04g52074.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.718; most accessible tissue: Minghui63 flower, score: 78.426 |
| vg0430929924 (J) | chr04 | 30929924 | G | T | 76.40% | 0.00% | T -> G |
LOC_Os04g52074.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 67.171; most accessible tissue: Minghui63 flower, score: 80.339 |
|
| vg0430929963 (J) | chr04 | 30929963 | A | T | 94.10% | 0.00% | A -> T | NA |
LOC_Os04g52074.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 66.982; most accessible tissue: Callus, score: 77.468 |
| vg0430930025 (J) | chr04 | 30930025 | A | G | 99.60% | 0.00% | A -> G | NA |
LOC_Os04g52074.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 69.591; most accessible tissue: Minghui63 flag leaf, score: 81.052 |
| vg0430930305 (J) | chr04 | 30930305 | G | C | 94.10% | 0.00% | G -> C | NA |
LOC_Os04g52074.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 71.682; most accessible tissue: Minghui63 flag leaf, score: 83.412 |
| vg0430930578 (J) | chr04 | 30930578 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os04g52074.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 71.022; most accessible tissue: Minghui63 flower, score: 83.015 |
| vg0430930581 (J) | chr04 | 30930581 | A | G | 99.60% | 0.00% | A -> G | NA |
LOC_Os04g52074.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 70.470; most accessible tissue: Minghui63 flower, score: 82.376 |
| vg0430930592 (J) | chr04 | 30930592 | G | A | 95.40% | 0.00% | G -> A | NA |
LOC_Os04g52074.1 Alt: A| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 68.899; most accessible tissue: Minghui63 flower, score: 81.554 |
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