16 variations found. Os07g0646700/LOC_Os07g45250 (transposon protein; putative; unclassified; expressed), ranging from 27,001,733 bp to 27,004,314 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os07g45250 | transposon protein, putative, unclassified; RAP ID: Os07g0646700; MSU ID: LOC_Os07g45250 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0727001857 (J) | chr07 | 27001857 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os07g45194.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g45260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g45250.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.877; most accessible tissue: Zhenshan97 root, score: 80.680 |
| vg0727002006 (J) | chr07 | 27002006 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os07g45194.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g45260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g45250.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.425; most accessible tissue: Callus, score: 89.929 |
| vg0727002546 (J) | chr07 | 27002546 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os07g45250.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g45194.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g45260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 60.715; most accessible tissue: Callus, score: 88.336 |
| vg0727002572 (J) | chr07 | 27002572 | GT | G | 99.80% | 0.00% | GT -> G | NA |
LOC_Os07g45250.1 Alt: G| frameshift_variant HIGH(snpEff)
LOC_Os07g45194.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 61.163; most accessible tissue: Callus, score: 88.336 |
| vg0727002584 (J) | chr07 | 27002584 | CA | C | 98.80% | 0.00% | CA -> C | NA |
LOC_Os07g45250.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 58.571; most accessible tissue: Zhenshan97 flower, score: 74.953 |
| vg0727002951 (J) | chr07 | 27002951 | G | C | 99.60% | 0.00% | G -> C | NA |
LOC_Os07g45250.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 58.120; most accessible tissue: Callus, score: 85.205 |
| vg0727002986 (J) | chr07 | 27002986 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os07g45250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 61.906; most accessible tissue: Callus, score: 85.205 |
| vg0727003261 (J) | chr07 | 27003261 | A | AC | 98.10% | 0.00% | A -> ACAACTGAAC ATAG,ACAAC TGAACATAGA GTCG,ACAAC TGAACATAGA GTCGAGCCTT GTATTTGTGT AGCCCCCG,A C | NA |
LOC_Os07g45250.1 Alt: ACAACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCG| stop_gained&inframe_insertion HIGH(snpEff)/inframe_variant(CooVar)
LOC_Os07g45250.1 Alt: AC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os07g45250.1 Alt: ACAACTGAACATAGAGTCG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os07g45250.1 Alt: ACAACTGAACATAG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 60.987; most accessible tissue: Callus, score: 87.142 |
| vg0727003262 (J) | chr07 | 27003262 | A | C | 87.20% | 1.25% | A -> C | NA |
LOC_Os07g45250.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g45250.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 60.987; most accessible tissue: Callus, score: 87.142 |
| vg0727003263 (J) | chr07 | 27003263 | A | ACTGAAC ATAGAGT CGAGC | 99.60% | 0.00% | A -> ACTGAACATA GAGTCGAGC, ACTGAACATA GAGTCGAGCC TTGTATTTGT GTAGCCCCCG ACT | NA |
LOC_Os07g45250.1 Alt: ACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCGACT| stop_gained&disruptive_inframe_insertion HIGH(snpEff)
LOC_Os07g45194.1 Alt: ACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCGACT| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g45260.1 Alt: ACTGAACATAGAGTCGAGCCTTGTATTTGTGTAGCCCCCGACT| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g45250.1 Alt: ACTGAACATAGAGTCGAGC| stop_gained&disruptive_inframe_insertion HIGH(snpEff) LOC_Os07g45194.1 Alt: ACTGAACATAGAGTCGAGC| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g45260.1 Alt: ACTGAACATAGAGTCGAGC| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 60.614; most accessible tissue: Callus, score: 87.142 |
| vg0727003269 (J) | chr07 | 27003269 | C | T | 98.70% | 0.00% | C -> T | NA |
LOC_Os07g45250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 60.937; most accessible tissue: Callus, score: 87.142 |
| vg0727003501 (J) | chr07 | 27003501 | G | T | 98.80% | 0.00% | G -> T | NA |
LOC_Os07g45250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 61.124; most accessible tissue: Callus, score: 88.610 |
| vg0727003948 (J) | chr07 | 27003948 | A | G | 98.40% | 0.00% | A -> G | NA |
LOC_Os07g45250.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 61.786; most accessible tissue: Callus, score: 83.754 |
| vg0727003953 (J) | chr07 | 27003953 | C | T | 98.80% | 0.00% | C -> T | NA |
LOC_Os07g45250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 61.592; most accessible tissue: Callus, score: 83.754 |
| vg0727004024 (J) | chr07 | 27004024 | T | C | 98.40% | 0.00% | T -> C | NA |
LOC_Os07g45250.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 59.437; most accessible tissue: Callus, score: 83.754 |
| vg0727004290 (J) | chr07 | 27004290 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os07g45250.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g45194.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g45260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.675; most accessible tissue: Callus, score: 90.008 |