23 variations found. LOC_Os05g37540 (transposon protein; putative; unclassified; expressed), ranging from 21,975,435 bp to 21,979,388 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0521975499 (J) | chr05 | 21975499 | C | T | 37.60% | 53.53% | C -> T | NA |
LOC_Os05g37530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g37550.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g37540.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.787; most accessible tissue: Callus, score: 29.988 |
| vg0521975533 (J) | chr05 | 21975533 | GT | G | 39.30% | 54.40% | GT -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g37530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g37550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g37540.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.787; most accessible tissue: Callus, score: 29.988 |
| vg0521975611 (J) | chr05 | 21975611 | G | A | 37.30% | 54.17% | G -> A | NA |
LOC_Os05g37540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g37540.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.456; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0521975663 (J) | chr05 | 21975663 | A | G | 57.50% | 16.53% | A -> G | NA |
LOC_Os05g37540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g37540.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.456; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0521975787 (J) | chr05 | 21975787 | G | A | 46.30% | 20.69% | G -> A | NA |
LOC_Os05g37540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g37540.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 5.468; most accessible tissue: Callus, score: 15.475 |
| vg0521975971 (J) | chr05 | 21975971 | T | C | 39.40% | 51.25% | T -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g37530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g37550.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g37540.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.260; most accessible tissue: Callus, score: 24.036 |
|
| vg0521976037 (J) | chr05 | 21976037 | A | G | 38.60% | 44.12% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g37530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g37550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g37540.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.260; most accessible tissue: Callus, score: 24.036 |
| vg0521976073 (J) | chr05 | 21976073 | C | T | 59.50% | 0.19% | C -> T | NA |
LOC_Os05g37530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g37550.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g37540.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.260; most accessible tissue: Callus, score: 24.036 |
| vg0521976358 (J) | chr05 | 21976358 | TA | T | 39.20% | 40.63% | TA -> T | NA |
LOC_Os05g37550.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g37540.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.809; most accessible tissue: Zhenshan97 flower, score: 12.818 |
| vg0521976361 (J) | chr05 | 21976361 | A | T | 38.70% | 43.55% | A -> T | NA |
LOC_Os05g37550.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g37540.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.809; most accessible tissue: Zhenshan97 flower, score: 12.818 |
| vg0521976503 (J) | chr05 | 21976503 | A | C | 87.10% | 4.21% | A -> C | NA |
LOC_Os05g37540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g37540.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 6.806; most accessible tissue: Callus, score: 18.902 |
| vg0521976540 (J) | chr05 | 21976540 | G | A | 38.50% | 50.51% | G -> A | NA |
LOC_Os05g37540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g37540.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.806; most accessible tissue: Callus, score: 18.902 |
| vg0521976780 (J) | chr05 | 21976780 | T | C | 45.50% | 14.28% | T -> C | NA |
LOC_Os05g37540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g37540.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.540; most accessible tissue: Callus, score: 16.271 |
| vg0521976823 (J) | chr05 | 21976823 | A | G | 15.20% | 59.75% | A -> G | NA |
LOC_Os05g37540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g37540.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 5.540; most accessible tissue: Callus, score: 16.271 |
| vg0521977534 (J) | chr05 | 21977534 | C | T | 37.10% | 54.76% | C -> T | NA |
LOC_Os05g37540.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os05g37540.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.961; most accessible tissue: Callus, score: 7.887 |
| vg0521978609 (J) | chr05 | 21978609 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os05g37550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os05g37540.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.419; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0521978662 (J) | chr05 | 21978662 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os05g37550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os05g37540.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.419; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0521978696 (J) | chr05 | 21978696 | CA | TA | 38.50% | 56.52% | CA -> TA,C | NA |
LOC_Os05g37540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g37540.1 Alt: TA| stop_gained HIGH(snpEff)/stop_gained(CooVar) LOC_Os05g37540.1 Alt: C| frameshift_variant HIGH(snpEff) The average chromatin accessibility score: 4.419; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0521978698 (J) | chr05 | 21978698 | G | A | 38.70% | 59.88% | G -> A | NA |
LOC_Os05g37540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g37540.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.419; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0521979032 (J) | chr05 | 21979032 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os05g37540.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os05g37550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 7.775; most accessible tissue: Zhenshan97 flower, score: 12.818 |
| vg0521979033 (J) | chr05 | 21979033 | G | C | 97.50% | 0.00% | G -> C | NA |
LOC_Os05g37540.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 7.775; most accessible tissue: Zhenshan97 flower, score: 12.818 |
| vg0521979055 (J) | chr05 | 21979055 | T | C | 99.50% | 0.00% | T -> C | NA |
LOC_Os05g37540.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 7.775; most accessible tissue: Zhenshan97 flower, score: 12.818 |
| vg0521979295 (J) | chr05 | 21979295 | G | T | 82.70% | 1.50% | G -> T | NA |
LOC_Os05g37540.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g37540.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.123; most accessible tissue: Zhenshan97 flag leaf, score: 15.873 |