24 variations found. Os04g0532800/LOC_Os04g45020 (MYB family transcription factor; putative; expressed), ranging from 26,637,818 bp to 26,640,662 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os04g45020 | MYB family transcription factor, putative, expressed; RAP ID: Os04g0532800; MSU ID: LOC_Os04g45020 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0426637827 (J) | chr04 | 26637827 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os04g45020.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g45030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.887; most accessible tissue: Minghui63 root, score: 96.060 |
| vg0426638064 (J) | chr04 | 26638064 | ACGG | A | 96.00% | 0.00% | ACGG -> A | NA |
LOC_Os04g45020.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.326; most accessible tissue: Callus, score: 99.422 |
| vg0426638207 (J) | chr04 | 26638207 | C | T | 96.30% | 0.00% | C -> T | NA |
LOC_Os04g45020.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.610; most accessible tissue: Callus, score: 99.358 |
| vg0426638277 (J) | chr04 | 26638277 | C | T | 95.30% | 0.00% | C -> T,G | NA |
LOC_Os04g45020.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45020.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.149; most accessible tissue: Callus, score: 99.358 |
| vg0426638515 (J) | chr04 | 26638515 | T | C | 95.50% | 0.00% | T -> C | NA |
LOC_Os04g45030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.535; most accessible tissue: Callus, score: 91.835 |
| vg0426638588 (J) | chr04 | 26638588 | CT | C | 88.50% | 0.00% | CT -> C,CTT | NA |
LOC_Os04g45030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45020.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.545; most accessible tissue: Zhenshan97 flower, score: 80.904 |
| vg0426638625 (J) | chr04 | 26638625 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os04g45030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g45020.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 60.195; most accessible tissue: Zhenshan97 flower, score: 80.311 |
| vg0426638634 (J) | chr04 | 26638634 | A | AT | 95.50% | 0.00% | A -> AT | NA |
LOC_Os04g45030.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45020.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.867; most accessible tissue: Zhenshan97 flower, score: 80.006 |
| vg0426638684 (J) | chr04 | 26638684 | T | C | 95.50% | 0.00% | T -> C | NA |
LOC_Os04g45030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.561; most accessible tissue: Callus, score: 85.820 |
| vg0426638982 (J) | chr04 | 26638982 | AT | A | 95.50% | 0.00% | AT -> A | NA |
LOC_Os04g45030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.068; most accessible tissue: Zhenshan97 flower, score: 94.243 |
| vg0426639033 (J) | chr04 | 26639033 | C | CT | 95.40% | 0.00% | C -> CT,CTT | NA |
LOC_Os04g45040.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45040.3 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45020.1 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.3 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45020.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.647; most accessible tissue: Zhenshan97 flower, score: 94.601 |
| vg0426639190 (J) | chr04 | 26639190 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os04g45040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g45040.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g45040.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g45030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g45020.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 66.375; most accessible tissue: Zhenshan97 flower, score: 95.496 |
| vg0426639301 (J) | chr04 | 26639301 | T | C | 98.50% | 0.00% | T -> C | NA |
LOC_Os04g45040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45040.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.970; most accessible tissue: Minghui63 root, score: 96.290 |
| vg0426639668 (J) | chr04 | 26639668 | C | T | 86.80% | 0.00% | C -> T | NA |
LOC_Os04g45040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45040.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.789; most accessible tissue: Zhenshan97 flower, score: 92.219 |
| vg0426639685 (J) | chr04 | 26639685 | GA | GCA | 94.80% | 0.00% | GA -> GCA,GCAA,G ,GAA | NA |
LOC_Os04g45040.1 Alt: GCA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45040.3 Alt: GCA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.2 Alt: GCA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: GCA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45020.1 Alt: GCA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45020.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.1 Alt: GCAA| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g45040.3 Alt: GCAA| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g45040.2 Alt: GCAA| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g45030.1 Alt: GCAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g45020.1 Alt: GCAA| intron_variant MODIFIER(snpEff) LOC_Os04g45040.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.3 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.2 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45020.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.878; most accessible tissue: Zhenshan97 flower, score: 91.965 |
| vg0426639778 (J) | chr04 | 26639778 | A | G | 95.50% | 0.00% | A -> G | NA |
LOC_Os04g45040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45040.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45020.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.016; most accessible tissue: Zhenshan97 flower, score: 91.514 |
| vg0426640040 (J) | chr04 | 26640040 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os04g45020.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.771; most accessible tissue: Zhenshan97 flower, score: 91.792 |
| vg0426640044 (J) | chr04 | 26640044 | C | T | 95.50% | 0.00% | C -> T | NA |
LOC_Os04g45020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.854; most accessible tissue: Zhenshan97 flower, score: 91.821 |
| vg0426640200 (J) | chr04 | 26640200 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os04g45020.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.794; most accessible tissue: Minghui63 root, score: 92.448 |
| vg0426640217 (J) | chr04 | 26640217 | T | G | 95.50% | 0.00% | T -> G | NA |
LOC_Os04g45020.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 88.812; most accessible tissue: Minghui63 root, score: 92.273 |
| vg0426640431 (J) | chr04 | 26640431 | TC | T | 95.60% | 0.00% | TC -> T | NA |
LOC_Os04g45020.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.034; most accessible tissue: Zhenshan97 flower, score: 91.994 |
| vg0426640480 (J) | chr04 | 26640480 | A | T | 88.20% | 0.00% | A -> T | NA |
LOC_Os04g45020.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.207; most accessible tissue: Zhenshan97 flower, score: 92.566 |
| vg0426640592 (J) | chr04 | 26640592 | G | C | 95.50% | 0.00% | G -> C | NA |
LOC_Os04g45020.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g45040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45040.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g45030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.209; most accessible tissue: Zhenshan97 flower, score: 93.813 |
| STR0426640432 (J) | chr04 | 26640432 | CC | C | 97.70% | 0.00% | CC -> C | NA |
|