18 variations found. Os09g0433000/LOC_Os09g26310 (hypro1; putative; expressed), ranging from 15,896,374 bp to 15,898,021 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os09g26310 | hypro1, putative, expressed; RAP ID: Os09g0433000; MSU ID: LOC_Os09g26310 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0915896376 (J) | chr09 | 15896376 | A | T | 55.30% | 0.00% | A -> T |
LOC_Os09g26310.1 Alt: T| splice_region_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os09g26310.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.741; most accessible tissue: Zhenshan97 flower, score: 88.827 |
|
| vg0915896610 (J) | chr09 | 15896610 | A | AC | 91.70% | 6.94% | A -> AC,ACCCC,A CC,ACCC | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g26310.1 Alt: ACCC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26300.1 Alt: ACCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26310.1 Alt: ACC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26300.1 Alt: ACC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26310.1 Alt: AC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26300.1 Alt: AC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26310.1 Alt: ACCCC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26300.1 Alt: ACCCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.035; most accessible tissue: Zhenshan97 young leaf, score: 94.184 |
| vg0915896622 (J) | chr09 | 15896622 | T | C | 89.50% | 0.00% | T -> C | NA |
LOC_Os09g26310.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26300.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.424; most accessible tissue: Zhenshan97 young leaf, score: 94.220 |
| vg0915896701 (J) | chr09 | 15896701 | T | C | 99.20% | 0.00% | T -> C | NA |
LOC_Os09g26310.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26300.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.801; most accessible tissue: Zhenshan97 young leaf, score: 93.846 |
| vg0915896709 (J) | chr09 | 15896709 | C | G | 62.60% | 0.25% | G -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g26310.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26300.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.157; most accessible tissue: Zhenshan97 young leaf, score: 93.885 |
| vg0915896830 (J) | chr09 | 15896830 | C | A | 55.20% | 0.08% | C -> A |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g26310.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.680; most accessible tissue: Zhenshan97 young leaf, score: 92.818 |
|
| vg0915896950 (J) | chr09 | 15896950 | TGATCGA TC | TGATCGA TCGATC | 88.70% | 0.00% | TGATCGATC -> TGATCGATCG ATC,T | NA |
LOC_Os09g26310.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26310.1 Alt: TGATCGATCGATC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26300.1 Alt: TGATCGATCGATC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.818; most accessible tissue: Zhenshan97 flower, score: 90.807 |
| vg0915896979 (J) | chr09 | 15896979 | A | G | 99.20% | 0.00% | A -> G | NA |
LOC_Os09g26310.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.281; most accessible tissue: Zhenshan97 young leaf, score: 91.689 |
| vg0915897224 (J) | chr09 | 15897224 | CGT | TGT | 55.00% | 0.00% | CGT -> TGT,C |
LOC_Os09g26310.1 Alt: TGT| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g26310.1 Alt: C| frameshift_variant HIGH(snpEff) The average chromatin accessibility score: 87.368; most accessible tissue: Zhenshan97 flower, score: 95.746 |
|
| vg0915897401 (J) | chr09 | 15897401 | G | C | 99.20% | 0.00% | G -> C | NA |
LOC_Os09g26310.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.581; most accessible tissue: Zhenshan97 flower, score: 97.248 |
| vg0915897529 (J) | chr09 | 15897529 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os09g26310.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.785; most accessible tissue: Zhenshan97 flower, score: 96.906 |
| vg0915897691 (J) | chr09 | 15897691 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os09g26310.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.847; most accessible tissue: Zhenshan97 flower, score: 96.941 |
| vg0915897752 (J) | chr09 | 15897752 | G | A | 62.80% | 0.00% | A -> G | NA |
LOC_Os09g26310.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.948; most accessible tissue: Zhenshan97 flower, score: 97.688 |
| vg0915897845 (J) | chr09 | 15897845 | G | T | 55.40% | 0.00% | G -> T | NA |
LOC_Os09g26310.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.438; most accessible tissue: Zhenshan97 flower, score: 98.513 |
| vg0915897991 (J) | chr09 | 15897991 | CTAATCA AGCTCAC G | C | 93.70% | 0.00% | CTAATCAAGC TCACG -> C | NA |
LOC_Os09g26310.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 92.459; most accessible tissue: Zhenshan97 flower, score: 99.047 |
| vg0915898002 (J) | chr09 | 15898002 | C | T | 54.50% | 0.00% | C -> T |
LOC_Os09g26310.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 92.359; most accessible tissue: Zhenshan97 flower, score: 99.032 |
|
| vg0915898007 (J) | chr09 | 15898007 | AATCAAG AATTCCA TT | A | 99.20% | 0.00% | AATCAAGAAT TCCATT -> A | NA |
LOC_Os09g26310.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26310.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26310-LOC_Os09g26320 Alt: A| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g26310.1 Alt: A| non_coding_transcript_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.347; most accessible tissue: Zhenshan97 flower, score: 99.032 |
| STR0915897842 (J) | chr09 | 15897842 | GAGG | GAGT | 52.60% | 0.00% | GAGG -> GAGT | NA |
|