16 variations found. LOC_Os03g51320 (retrotransposon protein; putative; unclassified; expressed), ranging from 29,360,286 bp to 29,363,577 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0329361287 (J) | chr03 | 29361287 | C | G | 70.70% | 15.81% | C -> G | NA |
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g51320.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 20.534; most accessible tissue: Zhenshan97 flag leaf, score: 56.010 |
| vg0329361593 (J) | chr03 | 29361593 | G | A | 56.80% | 40.69% | G -> A | NA |
LOC_Os03g51320.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 31.615; most accessible tissue: Zhenshan97 flower, score: 70.106 |
| vg0329361666 (J) | chr03 | 29361666 | T | C | 56.60% | 19.36% | T -> C | NA |
LOC_Os03g51320.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 32.821; most accessible tissue: Zhenshan97 flower, score: 72.863 |
| vg0329361688 (J) | chr03 | 29361688 | G | A | 69.40% | 16.17% | G -> A | NA |
LOC_Os03g51320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 34.951; most accessible tissue: Zhenshan97 flower, score: 75.194 |
| vg0329361713 (J) | chr03 | 29361713 | A | G | 56.00% | 43.33% | A -> G | NA |
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g51320.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 35.365; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 |
| vg0329361717 (J) | chr03 | 29361717 | G | A | 56.20% | 43.14% | G -> A | NA |
LOC_Os03g51320.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 35.377; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 |
| vg0329362069 (J) | chr03 | 29362069 | T | A | 56.10% | 42.91% | T -> A | NA |
LOC_Os03g51320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 32.311; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 |
| vg0329362085 (J) | chr03 | 29362085 | C | T | 55.90% | 42.51% | C -> T | NA |
LOC_Os03g51320.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 29.123; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 |
| vg0329362446 (J) | chr03 | 29362446 | C | T | 56.80% | 41.58% | C -> T | NA |
LOC_Os03g51320.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 26.118; most accessible tissue: Zhenshan97 root, score: 59.664 |
| vg0329362884 (J) | chr03 | 29362884 | G | A | 52.40% | 42.28% | G -> A | NA |
LOC_Os03g51320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 28.374; most accessible tissue: Zhenshan97 flag leaf, score: 63.670 |
| vg0329362963 (J) | chr03 | 29362963 | C | T | 56.70% | 40.61% | C -> T | NA |
LOC_Os03g51310.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51320.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 30.009; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 |
| vg0329363053 (J) | chr03 | 29363053 | A | T | 21.60% | 45.60% | A -> T | NA |
LOC_Os03g51320.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 30.522; most accessible tissue: Zhenshan97 flag leaf, score: 69.582 |
| vg0329363160 (J) | chr03 | 29363160 | G | A | 56.80% | 41.09% | G -> A | NA |
LOC_Os03g51320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 25.615; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 |
| vg0329363247 (J) | chr03 | 29363247 | G | C | 55.90% | 43.38% | G -> C | NA |
LOC_Os03g51320.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 24.884; most accessible tissue: Zhenshan97 flag leaf, score: 63.670 |
| vg0329363433 (J) | chr03 | 29363433 | T | C | 56.70% | 42.19% | T -> C | NA |
LOC_Os03g51320.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 25.675; most accessible tissue: Zhenshan97 flag leaf, score: 65.300 |
| vg0329363518 (J) | chr03 | 29363518 | G | A | 48.20% | 39.82% | G -> A | NA |
LOC_Os03g51320.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g51320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.737; most accessible tissue: Zhenshan97 panicle, score: 59.590 |