35 variations found. LOC_Os08g19400 (retrotransposon protein; putative; unclassified; expressed), ranging from 11,598,894 bp to 11,600,329 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0811598906 (J) | chr08 | 11598906 | C | T | 36.50% | 54.91% | C -> T | NA |
LOC_Os08g19400.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 14.137; most accessible tissue: Zhenshan97 flower, score: 20.672 |
| vg0811598961 (J) | chr08 | 11598961 | C | T | 34.90% | 60.60% | C -> T | NA |
LOC_Os08g19400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 17.049; most accessible tissue: Zhenshan97 flower, score: 29.832 |
| vg0811599014 (J) | chr08 | 11599014 | G | T | 37.50% | 59.65% | G -> T | NA |
LOC_Os08g19400.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.080; most accessible tissue: Zhenshan97 flower, score: 30.815 |
| vg0811599017 (J) | chr08 | 11599017 | C | A | 20.90% | 66.86% | C -> A | NA |
LOC_Os08g19400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 18.990; most accessible tissue: Zhenshan97 flower, score: 29.832 |
| vg0811599207 (J) | chr08 | 11599207 | C | Unkown | 48.80% | 48.88% | C -> T | NA |
LOC_Os08g19400.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os08g19380.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os08g19410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os08g19390.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 21.523; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 |
| vg0811599210 (J) | chr08 | 11599210 | C | A | 47.90% | 48.96% | C -> A | NA |
LOC_Os08g19400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.610; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 |
| vg0811599213 (J) | chr08 | 11599213 | G | C | 48.50% | 48.98% | G -> C | NA |
LOC_Os08g19400.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.610; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 |
| vg0811599216 (J) | chr08 | 11599216 | G | A | 43.70% | 49.13% | G -> A | NA |
LOC_Os08g19400.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.265; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 |
| vg0811599219 (J) | chr08 | 11599219 | C | T | 47.60% | 49.17% | C -> T | NA |
LOC_Os08g19400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.193; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 |
| vg0811599230 (J) | chr08 | 11599230 | C | T | 47.80% | 48.96% | C -> T | NA |
LOC_Os08g19400.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 20.420; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 |
| vg0811599240 (J) | chr08 | 11599240 | C | T | 47.00% | 49.07% | C -> T,A | NA |
LOC_Os08g19400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 20.387; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 |
| vg0811599249 (J) | chr08 | 11599249 | GC | G | 47.90% | 48.92% | GC -> G | NA |
LOC_Os08g19400.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 20.279; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 |
| vg0811599267 (J) | chr08 | 11599267 | G | A | 48.10% | 48.88% | G -> A | NA |
LOC_Os08g19400.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 20.351; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 |
| vg0811599465 (J) | chr08 | 11599465 | C | A | 0.20% | 94.96% | C -> A | NA |
LOC_Os08g19400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.537; most accessible tissue: Zhenshan97 flag leaf, score: 32.264 |
| vg0811599467 (J) | chr08 | 11599467 | C | G | 0.20% | 95.87% | G -> C | NA |
LOC_Os08g19400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.968; most accessible tissue: Zhenshan97 flag leaf, score: 32.264 |
| vg0811599474 (J) | chr08 | 11599474 | A | G | 0.10% | 95.49% | G -> A | NA |
LOC_Os08g19400.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 20.160; most accessible tissue: Zhenshan97 root, score: 32.766 |
| vg0811599476 (J) | chr08 | 11599476 | T | C | 0.20% | 95.66% | C -> T | NA |
LOC_Os08g19400.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 20.160; most accessible tissue: Zhenshan97 root, score: 32.766 |
| vg0811599488 (J) | chr08 | 11599488 | C | T | 0.50% | 96.42% | T -> C | NA |
LOC_Os08g19400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.773; most accessible tissue: Zhenshan97 root, score: 32.766 |
| vg0811599496 (J) | chr08 | 11599496 | C | A | 1.40% | 83.37% | C -> A | NA |
LOC_Os08g19400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 17.671; most accessible tissue: Zhenshan97 root, score: 30.989 |
| vg0811599502 (J) | chr08 | 11599502 | A | T | 0.60% | 95.66% | T -> A | NA |
LOC_Os08g19400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 17.766; most accessible tissue: Zhenshan97 root, score: 32.766 |
| vg0811599505 (J) | chr08 | 11599505 | G | A | 0.60% | 95.32% | A -> G | NA |
LOC_Os08g19400.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 17.325; most accessible tissue: Zhenshan97 root, score: 30.989 |
| vg0811599507 (J) | chr08 | 11599507 | T | C | 0.60% | 95.58% | C -> T | NA |
LOC_Os08g19400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 17.245; most accessible tissue: Zhenshan97 root, score: 30.989 |
| vg0811599533 (J) | chr08 | 11599533 | T | C | 1.00% | 94.22% | C -> T | NA |
LOC_Os08g19400.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.662; most accessible tissue: Zhenshan97 root, score: 29.203 |
| vg0811599568 (J) | chr08 | 11599568 | A | G | 2.80% | 94.20% | A -> G | NA |
LOC_Os08g19400.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.824; most accessible tissue: Zhenshan97 root, score: 29.203 |
| vg0811599573 (J) | chr08 | 11599573 | T | A | 3.00% | 94.18% | T -> A | NA |
LOC_Os08g19400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.881; most accessible tissue: Zhenshan97 root, score: 29.203 |
| vg0811599605 (J) | chr08 | 11599605 | C | T | 0.90% | 82.50% | C -> T | NA |
LOC_Os08g19400.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.861; most accessible tissue: Zhenshan97 root, score: 30.989 |
| vg0811599636 (J) | chr08 | 11599636 | C | T | 0.50% | 90.80% | C -> T | NA |
LOC_Os08g19400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g19400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 17.158; most accessible tissue: Zhenshan97 root, score: 30.989 |
| vg0811599863 (J) | chr08 | 11599863 | A | G | 2.40% | 94.92% | A -> G | NA |
LOC_Os08g19380.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g19410.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19390.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19400.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 13.423; most accessible tissue: Zhenshan97 root, score: 23.888 |
| vg0811599869 (J) | chr08 | 11599869 | A | G | 2.40% | 94.92% | A -> G | NA |
LOC_Os08g19380.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g19410.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19390.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19400.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.848; most accessible tissue: Zhenshan97 young leaf, score: 18.248 |
| vg0811599914 (J) | chr08 | 11599914 | T | G | 2.40% | 94.14% | T -> G | NA |
LOC_Os08g19380.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g19410.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19390.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19400.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.063; most accessible tissue: Zhenshan97 young leaf, score: 16.877 |
| vg0811599918 (J) | chr08 | 11599918 | T | C | 2.40% | 94.22% | T -> C | NA |
LOC_Os08g19380.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g19410.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19390.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19400.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.063; most accessible tissue: Zhenshan97 young leaf, score: 16.877 |
| vg0811599925 (J) | chr08 | 11599925 | G | A | 5.00% | 91.52% | G -> A | NA |
LOC_Os08g19380.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g19410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19390.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19400.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.773; most accessible tissue: Zhenshan97 young leaf, score: 16.877 |
| vg0811599927 (J) | chr08 | 11599927 | G | A | 5.00% | 91.43% | G -> A | NA |
LOC_Os08g19380.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g19410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19390.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19400.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.773; most accessible tissue: Zhenshan97 young leaf, score: 16.877 |
| vg0811599950 (J) | chr08 | 11599950 | G | A | 2.30% | 94.12% | G -> A | NA |
LOC_Os08g19380.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g19410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19390.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19400.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 11.514; most accessible tissue: Zhenshan97 panicle, score: 20.424 |
| vg0811599981 (J) | chr08 | 11599981 | T | C | 2.90% | 93.59% | T -> C | NA |
LOC_Os08g19380.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g19410.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19390.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g19400.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 11.011; most accessible tissue: Zhenshan97 panicle, score: 20.424 |