21 variations found. LOC_Os03g35670 (retrotransposon protein; putative; unclassified), ranging from 19,756,608 bp to 19,759,145 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0319756963 (J) | chr03 | 19756963 | G | A | 29.70% | 66.61% | G -> A | NA |
LOC_Os03g35670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0319757071 (J) | chr03 | 19757071 | G | A | 31.80% | 63.52% | G -> A | NA |
LOC_Os03g35670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0319757074 (J) | chr03 | 19757074 | G | A | 31.50% | 66.04% | G -> A | NA |
LOC_Os03g35670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0319757099 (J) | chr03 | 19757099 | TG | T | 33.50% | 62.44% | TG -> T | NA |
LOC_Os03g35670.1 Alt: T/frameshift_variant(CooVar)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0319757112 (J) | chr03 | 19757112 | C | CT | 33.50% | 62.36% | C -> CT | NA |
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g35670.1 Alt: CT/frameshift_variant(CooVar) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0319757114 (J) | chr03 | 19757114 | T | G | 33.80% | 64.05% | T -> G | NA |
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g35670.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0319757125 (J) | chr03 | 19757125 | A | T | 35.40% | 60.83% | A -> T | NA |
LOC_Os03g35670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0319757135 (J) | chr03 | 19757135 | G | A | 35.10% | 61.36% | G -> A | NA |
LOC_Os03g35670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0319757143 (J) | chr03 | 19757143 | A | T | 33.60% | 62.25% | A -> T | NA |
LOC_Os03g35670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0319757148 (J) | chr03 | 19757148 | G | C | 34.00% | 63.97% | G -> C | NA |
LOC_Os03g35670.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0319757473 (J) | chr03 | 19757473 | T | C | 33.00% | 64.09% | T -> C | NA |
LOC_Os03g35670.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.461; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0319757475 (J) | chr03 | 19757475 | C | T | 33.70% | 61.83% | C -> T | NA |
LOC_Os03g35670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.461; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0319757555 (J) | chr03 | 19757555 | C | T | 34.70% | 49.75% | C -> T | NA |
LOC_Os03g35670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.461; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0319757598 (J) | chr03 | 19757598 | C | T | 30.50% | 50.38% | C -> T | NA |
LOC_Os03g35670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.217; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0319757767 (J) | chr03 | 19757767 | G | A | 31.30% | 52.03% | G -> A | NA |
LOC_Os03g35670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.634; most accessible tissue: Minghui63 young leaf, score: 8.301 |
| vg0319757909 (J) | chr03 | 19757909 | T | C | 32.80% | 60.75% | T -> C | NA |
LOC_Os03g35670.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.991; most accessible tissue: Minghui63 flower, score: 7.958 |
| vg0319757925 (J) | chr03 | 19757925 | T | C | 32.20% | 62.04% | T -> C | NA |
LOC_Os03g35670.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.394; most accessible tissue: Minghui63 flower, score: 7.958 |
| vg0319758392 (J) | chr03 | 19758392 | A | G | 30.40% | 50.85% | A -> G | NA |
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g35670.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 5.314; most accessible tissue: Callus, score: 10.812 |
| vg0319758657 (J) | chr03 | 19758657 | A | T | 31.20% | 65.85% | A -> T | NA |
LOC_Os03g35670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.354; most accessible tissue: Callus, score: 12.211 |
| vg0319758680 (J) | chr03 | 19758680 | C | A | 34.70% | 49.70% | C -> A | NA |
LOC_Os03g35670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.944; most accessible tissue: Callus, score: 18.700 |
| vg0319758726 (J) | chr03 | 19758726 | C | T | 28.00% | 52.18% | C -> T | NA |
LOC_Os03g35670.1 Alt: T/stop_gained(CooVar)
LOC_Os03g35670.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.031; most accessible tissue: Callus, score: 18.700 |