21 variations found. LOC_Os03g31190 (retrotransposon protein; putative; Ty1-copia subclass), ranging from 17,761,617 bp to 17,762,067 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761620 (J) | chr03 | 17761620 | A | C | 34.00% | 64.28% | A -> C | NA |
LOC_Os03g31190.1 Alt: C| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 35.807; most accessible tissue: Minghui63 panicle, score: 59.629 |
| vg0317761623 (J) | chr03 | 17761623 | CTG | C | 33.80% | 57.81% | CTG -> C,CTTG | NA |
LOC_Os03g31190.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os03g31190.1 Alt: CTTG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 34.958; most accessible tissue: Minghui63 panicle, score: 59.629 |
| vg0317761624 (J) | chr03 | 17761624 | TGTTGGA AA | TTGTAGA TCACTCG TTGGAAA | 36.70% | 39.38% | TGTTGGAAA -> TTGTAGATCA CTCGTTGGAA A,T,TTATAG ATCACTCGTT GGAAA,TTAT AGTTGGAAA | NA |
LOC_Os03g31190.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os03g31190.1 Alt: TTATAGTTGGAAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os03g31190.1 Alt: TTATAGATCACTCGTTGGAAA| stop_gained&disruptive_inframe_insertion HIGH(snpEff)/inframe_variant(CooVar) LOC_Os03g31190.1 Alt: TTGTAGATCACTCGTTGGAAA| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 34.876; most accessible tissue: Minghui63 panicle, score: 59.629 |
| vg0317761625 (J) | chr03 | 17761625 | G | GTAGATC ACTCGT | 33.10% | 64.18% | G -> GTAGATCACT CGT,GATCAC TCGT | NA |
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g31190.1 Alt: GTAGATCACTCGT| stop_gained&inframe_insertion HIGH(snpEff)/inframe_variant(CooVar) LOC_Os03g31190.1 Alt: GATCACTCGT| stop_gained&inframe_insertion HIGH(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 34.876; most accessible tissue: Minghui63 panicle, score: 59.629 |
| vg0317761627 (J) | chr03 | 17761627 | T | A | 33.90% | 61.68% | T -> A | NA |
LOC_Os03g31190.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 34.876; most accessible tissue: Minghui63 panicle, score: 59.629 |
| vg0317761628 (J) | chr03 | 17761628 | G | GTA | 33.30% | 62.51% | G -> GTA,A | NA |
LOC_Os03g31190.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g31190.1 Alt: GTA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 34.815; most accessible tissue: Minghui63 panicle, score: 59.629 |
| vg0317761629 (J) | chr03 | 17761629 | G | T | 33.90% | 59.80% | G -> T | NA |
LOC_Os03g31190.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 34.815; most accessible tissue: Minghui63 panicle, score: 59.629 |
| vg0317761631 (J) | chr03 | 17761631 | A | G | 33.50% | 60.37% | A -> G | NA |
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g31190.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 34.815; most accessible tissue: Minghui63 panicle, score: 59.629 |
| vg0317761695 (J) | chr03 | 17761695 | TGTAGGG TGATCTT AACATAA CCA | T | 19.40% | 67.92% | TGTAGGGTGA TCTTAACATA ACCA -> T | NA |
LOC_Os03g31190.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.954; most accessible tissue: Minghui63 panicle, score: 42.799 |
| vg0317761795 (J) | chr03 | 17761795 | TAGAACA GGAACA | T | 32.20% | 63.46% | TAGAACAGGA ACA -> T | NA |
LOC_Os03g31190.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 14.587; most accessible tissue: Minghui63 panicle, score: 29.741 |
| vg0317761884 (J) | chr03 | 17761884 | G | A | 31.50% | 64.30% | G -> A | NA |
LOC_Os03g31190.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.505; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg0317761940 (J) | chr03 | 17761940 | C | T | 36.40% | 49.87% | C -> T | NA |
LOC_Os03g31190.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg0317761982 (J) | chr03 | 17761982 | C | G | 50.80% | 42.64% | C -> G | NA |
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g31190.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg0317761986 (J) | chr03 | 17761986 | CTCCGGA | C | 50.60% | 42.59% | CTCCGGA -> C | NA |
LOC_Os03g31190.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg0317762015 (J) | chr03 | 17762015 | G | A | 40.40% | 39.12% | G -> A | NA |
LOC_Os03g31190.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg0317762020 (J) | chr03 | 17762020 | C | T | 52.40% | 42.19% | C -> T | NA |
LOC_Os03g31190.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg0317762025 (J) | chr03 | 17762025 | G | T | 51.70% | 44.12% | G -> T | NA |
LOC_Os03g31190.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg0317762026 (J) | chr03 | 17762026 | C | A | 51.70% | 44.20% | C -> A | NA |
LOC_Os03g31190.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg0317762038 (J) | chr03 | 17762038 | G | A | 47.20% | 46.23% | G -> A | NA |
LOC_Os03g31190.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg0317762042 (J) | chr03 | 17762042 | G | A | 36.60% | 53.72% | G -> A | NA |
LOC_Os03g31190.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 |
| vg0317762046 (J) | chr03 | 17762046 | T | A | 36.60% | 53.60% | T -> A | NA |
LOC_Os03g31190.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g31190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.609; most accessible tissue: Minghui63 flag leaf, score: 9.254 |