18 variations found. LOC_Os02g06520 (OsFBLD1 - F-box; LRR and FBD domain containing protein; expressed), ranging from 3,254,924 bp to 3,256,939 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0203254991 (J) | chr02 | 3254991 | TGAGAGA | TGAGAGA GA | 74.70% | 0.00% | TGAGAGA -> TGAGA,TGAG AGAGA,T | NA |
LOC_Os02g06520.1 Alt: TGAGA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06510.1 Alt: TGAGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06520.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06510.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06520.1 Alt: TGAGAGAGA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06510.1 Alt: TGAGAGAGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.760; most accessible tissue: Minghui63 root, score: 99.870 |
| vg0203255003 (J) | chr02 | 3255003 | A | AGAGAG | 65.70% | 2.43% | AGAGAG -> A | NA |
LOC_Os02g06520.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06510.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.755; most accessible tissue: Minghui63 root, score: 99.863 |
| vg0203255005 (J) | chr02 | 3255005 | AGAG | A | 82.50% | 4.46% | AGAG -> A,AGGAG | NA |
LOC_Os02g06520.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06510.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06520.1 Alt: AGGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06510.1 Alt: AGGAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 99.748; most accessible tissue: Minghui63 root, score: 99.857 |
| vg0203255022 (J) | chr02 | 3255022 | A | AC | 79.80% | 0.00% | A -> AGGAGGAC,A C,AGGAC | NA |
LOC_Os02g06520.1 Alt: AC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06510.1 Alt: AC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06520.1 Alt: AGGAC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06510.1 Alt: AGGAC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06520.1 Alt: AGGAGGAC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06510.1 Alt: AGGAGGAC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.737; most accessible tissue: Minghui63 root, score: 99.840 |
| vg0203255036 (J) | chr02 | 3255036 | C | G | 99.30% | 0.00% | C -> G | NA |
LOC_Os02g06520.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06510.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.713; most accessible tissue: Zhenshan97 flag leaf, score: 99.816 |
| vg0203255069 (J) | chr02 | 3255069 | A | C | 73.30% | 0.00% | C -> A | NA |
LOC_Os02g06520.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06510.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.583; most accessible tissue: Zhenshan97 flag leaf, score: 99.765 |
| vg0203255102 (J) | chr02 | 3255102 | G | T | 91.20% | 0.00% | G -> T |
LOC_Os02g06520.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g06520.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06510.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.708; most accessible tissue: Zhenshan97 flag leaf, score: 99.760 |
|
| vg0203255339 (J) | chr02 | 3255339 | A | G | 61.00% | 2.98% | G -> A | NA |
LOC_Os02g06520.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g06520.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 94.528; most accessible tissue: Zhenshan97 flag leaf, score: 99.259 |
| vg0203255417 (J) | chr02 | 3255417 | C | T | 89.80% | 1.61% | T -> C | NA |
LOC_Os02g06520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g06520.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 93.861; most accessible tissue: Zhenshan97 flag leaf, score: 99.167 |
| vg0203255491 (J) | chr02 | 3255491 | T | C | 64.80% | 3.00% | C -> T | NA |
LOC_Os02g06520.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06520.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 94.738; most accessible tissue: Zhenshan97 flag leaf, score: 98.754 |
| vg0203255590 (J) | chr02 | 3255590 | T | C | 71.10% | 0.00% | C -> T |
LOC_Os02g06520.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.328; most accessible tissue: Zhenshan97 flag leaf, score: 98.539 |
|
| vg0203255779 (J) | chr02 | 3255779 | G | C | 68.60% | 0.00% | C -> G | NA |
LOC_Os02g06520.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.771; most accessible tissue: Minghui63 flag leaf, score: 97.410 |
| vg0203255874 (J) | chr02 | 3255874 | G | T | 94.20% | 0.00% | T -> G | NA |
LOC_Os02g06520.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.124; most accessible tissue: Zhenshan97 flag leaf, score: 96.614 |
| vg0203256350 (J) | chr02 | 3256350 | G | A | 93.30% | 0.00% | G -> A | NA |
LOC_Os02g06510.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.317; most accessible tissue: Minghui63 flag leaf, score: 89.523 |
| vg0203256467 (J) | chr02 | 3256467 | C | T | 90.10% | 0.00% | C -> T | NA |
LOC_Os02g06520.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 76.127; most accessible tissue: Minghui63 flag leaf, score: 87.854 |
| vg0203256743 (J) | chr02 | 3256743 | G | C | 97.90% | 0.00% | G -> C | NA |
LOC_Os02g06520.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 67.143; most accessible tissue: Callus, score: 86.214 |
| vg0203256759 (J) | chr02 | 3256759 | A | G | 94.30% | 0.00% | G -> A | NA |
LOC_Os02g06520.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 67.171; most accessible tissue: Callus, score: 86.214 |
| vg0203256814 (J) | chr02 | 3256814 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os02g06520.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06510.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.906; most accessible tissue: Callus, score: 86.214 |
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