14 variations found. LOC_Os07g17510 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 10,346,890 bp to 10,352,129 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0710346937 (J) | chr07 | 10346937 | G | A | 7.30% | 74.59% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g17510.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g17500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.443; most accessible tissue: Minghui63 young leaf, score: 8.301 |
| vg0710347339 (J) | chr07 | 10347339 | A | G | 5.80% | 71.16% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g17500.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g17510.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.509; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg0710347343 (J) | chr07 | 10347343 | A | G | 5.50% | 70.78% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g17500.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g17510.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.509; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg0710348072 (J) | chr07 | 10348072 | C | T | 30.00% | 65.30% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g17500.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g17520.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g17510.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.679; most accessible tissue: Callus, score: 17.802 |
| vg0710348222 (J) | chr07 | 10348222 | T | G | 19.90% | 63.94% | T -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g17500.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g17520.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g17510.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.963; most accessible tissue: Callus, score: 9.925 |
| vg0710348320 (J) | chr07 | 10348320 | C | T | 30.40% | 63.18% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g17500.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g17520.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g17510.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.963; most accessible tissue: Callus, score: 9.925 |
| vg0710349296 (J) | chr07 | 10349296 | G | A | 31.40% | 64.52% | G -> A | NA |
LOC_Os07g17510.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g17510.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.695; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0710349951 (J) | chr07 | 10349951 | C | T | 29.70% | 63.56% | C -> T | NA |
LOC_Os07g17510.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g17510.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.776; most accessible tissue: Callus, score: 7.869 |
| vg0710349963 (J) | chr07 | 10349963 | GTACTTA CCACTGC AGGCCGA TTCCAGC AGGA | G | 29.80% | 63.63% | GTACTTACCA CTGCAGGCCG ATTCCAGCAG GA -> G | NA |
LOC_Os07g17510.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g17510.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 4.776; most accessible tissue: Callus, score: 7.869 |
| vg0710350287 (J) | chr07 | 10350287 | C | A | 30.60% | 63.65% | C -> A | NA |
LOC_Os07g17510.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g17510.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.806; most accessible tissue: Callus, score: 10.028 |
| vg0710350320 (J) | chr07 | 10350320 | C | A | 31.80% | 61.36% | C -> A | NA |
LOC_Os07g17510.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g17510.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.924; most accessible tissue: Callus, score: 10.028 |
| vg0710350879 (J) | chr07 | 10350879 | G | A | 30.80% | 61.72% | G -> A | NA |
LOC_Os07g17510.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g17510.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.942; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0710351290 (J) | chr07 | 10351290 | G | A | 30.40% | 64.35% | G -> A | NA |
LOC_Os07g17510.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g17510.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.041; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0710351976 (J) | chr07 | 10351976 | C | T | 2.60% | 71.56% | C -> T | NA |
LOC_Os07g17510.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g17510.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.720; most accessible tissue: Minghui63 flower, score: 9.270 |