10 variations found. Os04g0520900/LOC_Os04g44030 (PPR repeat domain containing protein; putative; expressed), ranging from 26,090,647 bp to 26,093,773 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os04g44030 | PPR repeat domain containing protein, putative, expressed; RAP ID: Os04g0520900; MSU ID: LOC_Os04g44030 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0426092094 (J) | chr04 | 26092094 | A | G | 99.50% | 0.00% | A -> G | NA |
LOC_Os04g44030.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os04g44020.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 63.145; most accessible tissue: Minghui63 flag leaf, score: 80.241 |
| vg0426092328 (J) | chr04 | 26092328 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os04g44030.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g44020.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 57.976; most accessible tissue: Minghui63 flower, score: 72.046 |
| vg0426092387 (J) | chr04 | 26092387 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os04g44030.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g44020.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 56.229; most accessible tissue: Minghui63 flower, score: 69.893 |
| vg0426092775 (J) | chr04 | 26092775 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os04g44030.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g44050.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g44020.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.377; most accessible tissue: Callus, score: 83.453 |
| vg0426092791 (J) | chr04 | 26092791 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os04g44030.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g44050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.178; most accessible tissue: Callus, score: 83.453 |
| vg0426093015 (J) | chr04 | 26093015 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os04g44030.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g44050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.356; most accessible tissue: Callus, score: 76.389 |
| vg0426093552 (J) | chr04 | 26093552 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os04g44030.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g44050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 56.951; most accessible tissue: Callus, score: 82.041 |
| vg0426093698 (J) | chr04 | 26093698 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os04g44030.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g44050.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 49.562; most accessible tissue: Callus, score: 84.682 |
| vg0426093766 (J) | chr04 | 26093766 | CAAA | CAAAA | 33.70% | 1.67% | CAAAA -> CAAA,CAA,C A,C | NA |
LOC_Os04g44030.1 Alt: CA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g44050.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44030.1 Alt: CAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44050.1 Alt: CAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44030.1 Alt: CAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44050.1 Alt: CAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os04g44030.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.008; most accessible tissue: Callus, score: 84.682 |
| vg0426093767 (J) | chr04 | 26093767 | A | C | 93.70% | 0.00% | A -> C | NA |
LOC_Os04g44030.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g44050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.113; most accessible tissue: Callus, score: 84.682 |