26 variations found. LOC_Os04g51730 (retrotransposon protein; putative; unclassified; expressed), ranging from 30,653,188 bp to 30,655,189 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 |
---|---|---|---|---|---|---|---|---|---|
vg0430653203 (J) | chr04 | 30653203 | A | G | 13.60% | 58.63% | A -> G | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 8.608; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430653642 (J) | chr04 | 30653642 | A | G | 0.10% | 89.00% | G -> A | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430653672 (J) | chr04 | 30653672 | A | G | 74.60% | 17.05% | A -> G | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430653703 (J) | chr04 | 30653703 | C | T | 84.30% | 15.26% | C -> T | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430653708 (J) | chr04 | 30653708 | A | T | 84.20% | 15.26% | A -> T | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430653732 (J) | chr04 | 30653732 | G | A | 84.00% | 15.43% | G -> A | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430653739 (J) | chr04 | 30653739 | A | C | 82.70% | 15.36% | A -> C | NA |
LOC_Os04g51730.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430653744 (J) | chr04 | 30653744 | T | Unkown | 84.40% | 15.38% | T -> C | NA |
LOC_Os04g51730.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os04g51720.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g51740.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430653750 (J) | chr04 | 30653750 | T | A | 41.60% | 19.53% | T -> A | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430653768 (J) | chr04 | 30653768 | C | T | 65.70% | 18.45% | C -> T | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.246; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430653771 (J) | chr04 | 30653771 | G | A | 51.10% | 34.98% | G -> A | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.246; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430653774 (J) | chr04 | 30653774 | G | A | 47.00% | 37.96% | G -> A | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.246; most accessible tissue: Minghui63 panicle, score: 20.733 |
vg0430654071 (J) | chr04 | 30654071 | G | A | 84.10% | 15.09% | G -> A | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 |
vg0430654076 (J) | chr04 | 30654076 | C | T | 64.00% | 15.07% | C -> T | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 |
vg0430654080 (J) | chr04 | 30654080 | G | T | 47.40% | 16.76% | G -> T | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 |
vg0430654095 (J) | chr04 | 30654095 | C | T | 84.50% | 14.92% | C -> T | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 |
vg0430654098 (J) | chr04 | 30654098 | A | G | 84.30% | 15.09% | A -> G | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 |
vg0430654100 (J) | chr04 | 30654100 | C | T | 84.60% | 14.92% | C -> T | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 |
vg0430654111 (J) | chr04 | 30654111 | T | C | 84.10% | 15.02% | T -> C | NA |
LOC_Os04g51730.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 |
vg0430654119 (J) | chr04 | 30654119 | G | A | 84.70% | 14.90% | G -> A | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 |
vg0430654148 (J) | chr04 | 30654148 | G | A | 76.00% | 16.80% | G -> A | NA |
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 |
vg0430654182 (J) | chr04 | 30654182 | T | C | 14.00% | 51.40% | T -> C | NA |
LOC_Os04g51730.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 |
vg0430654505 (J) | chr04 | 30654505 | A | G | 13.20% | 63.39% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g51720.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g51740.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g51730.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.261; most accessible tissue: Minghui63 flower, score: 7.958 |
vg0430654546 (J) | chr04 | 30654546 | A | G | 13.30% | 58.29% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g51720.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g51740.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g51730.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.654; most accessible tissue: Minghui63 flower, score: 7.958 |
vg0430654714 (J) | chr04 | 30654714 | TA | T | 4.20% | 57.24% | TA -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g51720.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g51740.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g51730.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.888; most accessible tissue: Minghui63 flag leaf, score: 11.122 |
vg0430654813 (J) | chr04 | 30654813 | A | G | 13.80% | 56.94% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g51720.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g51740.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g51730.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.435; most accessible tissue: Minghui63 flag leaf, score: 13.491 |