18 variations found. LOC_Os04g17520 (retrotransposon; putative; centromere-specific), ranging from 9,586,151 bp to 9,586,864 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 |
---|---|---|---|---|---|---|---|---|---|
vg0409586287 (J) | chr04 | 9586287 | G | A | 24.70% | 53.05% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.266; most accessible tissue: Minghui63 young leaf, score: 8.301 |
vg0409586309 (J) | chr04 | 9586309 | TA | T | 26.80% | 49.85% | TA -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.859; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0409586319 (J) | chr04 | 9586319 | C | T | 27.00% | 49.09% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.859; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0409586345 (J) | chr04 | 9586345 | C | T | 34.10% | 46.42% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.551; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0409586364 (J) | chr04 | 9586364 | C | T | 4.10% | 74.78% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.551; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0409586368 (J) | chr04 | 9586368 | AG | A | 2.50% | 82.46% | AG -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.551; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0409586370 (J) | chr04 | 9586370 | A | T | 2.50% | 82.16% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.551; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0409586432 (J) | chr04 | 9586432 | T | Unkown | 42.60% | 46.09% | T -> C | NA |
LOC_Os04g17510.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g17530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g17540.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g17520.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 6.646; most accessible tissue: Minghui63 root, score: 10.708 |
vg0409586482 (J) | chr04 | 9586482 | G | A | 46.90% | 41.13% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 9.709; most accessible tissue: Minghui63 panicle, score: 16.270 |
vg0409586493 (J) | chr04 | 9586493 | C | T | 38.00% | 42.04% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 9.856; most accessible tissue: Minghui63 panicle, score: 16.270 |
vg0409586505 (J) | chr04 | 9586505 | G | A | 28.80% | 44.58% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.262; most accessible tissue: Minghui63 root, score: 17.665 |
vg0409586681 (J) | chr04 | 9586681 | G | C | 54.60% | 41.39% | G -> C | NA |
LOC_Os04g17510.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 16.091; most accessible tissue: Minghui63 root, score: 29.362 |
vg0409586690 (J) | chr04 | 9586690 | A | G | 35.80% | 30.91% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 16.091; most accessible tissue: Minghui63 root, score: 29.362 |
vg0409586691 (J) | chr04 | 9586691 | G | A | 47.40% | 42.66% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 16.091; most accessible tissue: Minghui63 root, score: 29.362 |
vg0409586692 (J) | chr04 | 9586692 | C | A | 54.50% | 42.15% | C -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 16.091; most accessible tissue: Minghui63 root, score: 29.362 |
vg0409586716 (J) | chr04 | 9586716 | A | G | 54.50% | 42.00% | A -> G | NA |
LOC_Os04g17520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17520.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 16.014; most accessible tissue: Minghui63 root, score: 29.362 |
vg0409586728 (J) | chr04 | 9586728 | C | T | 51.80% | 42.62% | C -> T | NA |
LOC_Os04g17520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17520.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 16.014; most accessible tissue: Minghui63 root, score: 29.362 |
vg0409586830 (J) | chr04 | 9586830 | A | T | 23.10% | 68.85% | A -> T | NA |
LOC_Os04g17520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17520.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 15.542; most accessible tissue: Minghui63 root, score: 27.443 |