10 variations found. LOC_Os03g07234 (pentatricopeptide; putative; expressed), ranging from 3,700,038 bp to 3,701,586 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0303700054 (J) | chr03 | 3700054 | T | A | 90.80% | 0.28% | T -> A | NA |
LOC_Os03g07234.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g07234.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 43.528; most accessible tissue: Callus, score: 82.522 |
| vg0303700300 (J) | chr03 | 3700300 | A | G | 98.60% | 0.00% | A -> G | NA |
LOC_Os03g07234.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 53.020; most accessible tissue: Zhenshan97 young leaf, score: 79.783 |
| vg0303700315 (J) | chr03 | 3700315 | A | C | 65.00% | 0.00% | C -> A | NA |
LOC_Os03g07234.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 53.505; most accessible tissue: Zhenshan97 young leaf, score: 79.507 |
| vg0303700417 (J) | chr03 | 3700417 | C | A | 52.20% | 0.15% | C -> A |
LOC_Os03g07234.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g07234.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 60.270; most accessible tissue: Zhenshan97 young leaf, score: 82.982 |
|
| vg0303700632 (J) | chr03 | 3700632 | T | C | 98.60% | 0.00% | T -> C | NA |
LOC_Os03g07234.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 70.078; most accessible tissue: Zhenshan97 young leaf, score: 83.412 |
| vg0303700851 (J) | chr03 | 3700851 | C | T | 90.80% | 0.28% | C -> T | NA |
LOC_Os03g07234.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g07234.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 73.988; most accessible tissue: Zhenshan97 young leaf, score: 88.127 |
| vg0303701024 (J) | chr03 | 3701024 | G | A | 93.50% | 0.00% | G -> A | NA |
LOC_Os03g07234.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.459; most accessible tissue: Zhenshan97 flag leaf, score: 94.478 |
| vg0303701125 (J) | chr03 | 3701125 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os03g07234.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.600; most accessible tissue: Zhenshan97 flag leaf, score: 96.276 |
| vg0303701172 (J) | chr03 | 3701172 | G | A | 90.80% | 0.25% | G -> A | NA |
LOC_Os03g07234.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g07234.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 89.706; most accessible tissue: Zhenshan97 flag leaf, score: 96.423 |
| vg0303701536 (J) | chr03 | 3701536 | G | A | 65.10% | 0.00% | A -> G | NA |
LOC_Os03g07234.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.601; most accessible tissue: Zhenshan97 flag leaf, score: 97.526 |