16 variations found. Os04g0635100/LOC_Os04g54240 (wound induced protein; putative; expressed), ranging from 32,301,621 bp to 32,302,456 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os04g54240 | wound induced protein, putative, expressed; RAP ID: Os04g0635100; MSU ID: LOC_Os04g54240 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0432301621 (J) | chr04 | 32301621 | C | CT | 72.70% | 0.25% | C -> CT | NA |
LOC_Os04g54240.1 Alt: CT| splice_region_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os04g54240.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54230.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 49.603; most accessible tissue: Minghui63 panicle, score: 87.605 |
| vg0432301629 (J) | chr04 | 32301629 | C | T | 98.40% | 0.00% | C -> T | NA |
LOC_Os04g54240.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g54230.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.016; most accessible tissue: Minghui63 panicle, score: 87.238 |
| vg0432301638 (J) | chr04 | 32301638 | G | A | 67.80% | 0.00% | A -> G |
LOC_Os04g54240.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g54230.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.347; most accessible tissue: Minghui63 panicle, score: 87.238 |
|
| vg0432301656 (J) | chr04 | 32301656 | TA | T | 67.70% | 0.00% | T -> TA,TAA | NA |
LOC_Os04g54240.1 Alt: TAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g54230.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54240.1 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54230.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.539; most accessible tissue: Minghui63 panicle, score: 85.556 |
| vg0432301781 (J) | chr04 | 32301781 | G | GGTA | 74.00% | 0.30% | G -> GGTA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g54240.1 Alt: GGTA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54230.1 Alt: GGTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: GGTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.568; most accessible tissue: Minghui63 panicle, score: 89.702 |
| vg0432301849 (J) | chr04 | 32301849 | T | G | 73.50% | 0.00% | G -> T | NA |
LOC_Os04g54240.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g54230.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.718; most accessible tissue: Minghui63 panicle, score: 92.526 |
| vg0432302044 (J) | chr04 | 32302044 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os04g54240.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g54230.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54250.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.716; most accessible tissue: Minghui63 panicle, score: 97.778 |
| vg0432302126 (J) | chr04 | 32302126 | C | T | 72.70% | 0.15% | C -> T | NA |
LOC_Os04g54240.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g54240.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 89.687; most accessible tissue: Minghui63 panicle, score: 98.402 |
| vg0432302175 (J) | chr04 | 32302175 | C | T | 98.50% | 0.00% | C -> T | NA |
LOC_Os04g54240.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.966; most accessible tissue: Minghui63 panicle, score: 98.555 |
| vg0432302234 (J) | chr04 | 32302234 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os04g54240.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os04g54230.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54250.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.258; most accessible tissue: Minghui63 panicle, score: 98.884 |
| vg0432302385 (J) | chr04 | 32302385 | C | A | 91.70% | 0.00% | C -> A | NA |
LOC_Os04g54240.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g54230.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.661; most accessible tissue: Minghui63 panicle, score: 99.801 |
| vg0432302402 (J) | chr04 | 32302402 | G | A | 91.70% | 0.00% | G -> A | NA |
LOC_Os04g54240.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g54230.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.673; most accessible tissue: Minghui63 panicle, score: 99.798 |
| vg0432302417 (J) | chr04 | 32302417 | G | C | 99.80% | 0.00% | G -> C | NA |
LOC_Os04g54240.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g54230.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54250.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.849; most accessible tissue: Minghui63 panicle, score: 99.834 |
| vg0432302426 (J) | chr04 | 32302426 | A | T | 67.90% | 0.00% | T -> A |
LOC_Os04g54240.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g54230.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.462; most accessible tissue: Minghui63 panicle, score: 99.834 |
|
| vg0432302443 (J) | chr04 | 32302443 | G | A | 71.20% | 0.30% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g54240.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54230.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.513; most accessible tissue: Minghui63 panicle, score: 99.850 |
| vg0432302446 (J) | chr04 | 32302446 | G | T | 98.50% | 0.00% | G -> T | NA |
LOC_Os04g54240.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g54230.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54250.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.518; most accessible tissue: Minghui63 panicle, score: 99.850 |
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