16 variations found. LOC_Os01g04310 (transposon protein; putative; unclassified), ranging from 1,919,748 bp to 1,920,431 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0101920066 (J) | chr01 | 1920066 | G | A | 31.80% | 24.59% | G -> A | NA |
LOC_Os01g04310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.909; most accessible tissue: Callus, score: 26.447 |
| vg0101920299 (J) | chr01 | 1920299 | C | T | 59.40% | 33.03% | C -> T | NA |
LOC_Os01g04310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.136; most accessible tissue: Callus, score: 15.504 |
| vg0101920320 (J) | chr01 | 1920320 | T | C | 58.80% | 33.18% | T -> C | NA |
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g04310.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 9.027; most accessible tissue: Callus, score: 15.504 |
| vg0101920324 (J) | chr01 | 1920324 | A | G | 55.80% | 35.27% | A -> G | NA |
LOC_Os01g04310.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.027; most accessible tissue: Callus, score: 15.504 |
| vg0101920354 (J) | chr01 | 1920354 | A | G | 86.40% | 10.03% | A -> G | NA |
LOC_Os01g04310.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.780; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg0101920363 (J) | chr01 | 1920363 | C | T | 89.20% | 9.04% | C -> T | NA |
LOC_Os01g04310.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.146; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 |
| vg0101920370 (J) | chr01 | 1920370 | C | Unkown | 89.40% | 9.06% | C -> T | NA |
LOC_Os01g04310.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g04320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 7.146; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 |
| vg0101920377 (J) | chr01 | 1920377 | C | T | 89.40% | 8.99% | C -> T | NA |
LOC_Os01g04310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0101920381 (J) | chr01 | 1920381 | C | T | 89.00% | 8.97% | C -> T | NA |
LOC_Os01g04310.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0101920398 (J) | chr01 | 1920398 | C | A | 90.30% | 8.29% | C -> A,T | NA |
LOC_Os01g04310.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g04320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g04310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0101920404 (J) | chr01 | 1920404 | G | A | 89.40% | 8.80% | G -> A | NA |
LOC_Os01g04310.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0101920409 (J) | chr01 | 1920409 | A | G | 89.40% | 8.82% | A -> G | NA |
LOC_Os01g04310.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0101920420 (J) | chr01 | 1920420 | G | A | 89.20% | 8.87% | G -> A | NA |
LOC_Os01g04310.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0101920424 (J) | chr01 | 1920424 | C | CAT | 88.90% | 8.13% | C -> CAT | NA |
LOC_Os01g04310.1 Alt: CAT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0101920425 (J) | chr01 | 1920425 | A | C | 90.60% | 8.13% | A -> C | NA |
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g04310.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 7.607; most accessible tissue: Callus, score: 11.730 |
| vg0101920426 (J) | chr01 | 1920426 | T | C | 88.80% | 8.19% | T -> C | NA |
LOC_Os01g04310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g04310.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.607; most accessible tissue: Callus, score: 11.730 |