34 variations found. Os01g0627600/LOC_Os01g43720 (cytochrome P450 72A1; putative; expressed), ranging from 25,055,771 bp to 25,058,195 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g43720 | cytochrome P450 72A1, putative, expressed; RAP ID: Os01g0627600; MSU ID: LOC_Os01g43720 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0125055790 (J) | chr01 | 25055790 | T | C | 93.30% | 0.00% | T -> C |
LOC_Os01g43720.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43740.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.533; most accessible tissue: Callus, score: 92.843 |
|
| vg0125055806 (J) | chr01 | 25055806 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os01g43720.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g43740.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 64.420; most accessible tissue: Callus, score: 92.843 |
| vg0125055810 (J) | chr01 | 25055810 | C | T | 86.90% | 0.00% | C -> T | NA |
LOC_Os01g43720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.614; most accessible tissue: Callus, score: 92.843 |
| vg0125055835 (J) | chr01 | 25055835 | C | A | 97.10% | 0.61% | C -> A | NA |
LOC_Os01g43720.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43740.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 63.314; most accessible tissue: Zhenshan97 root, score: 88.851 |
| vg0125055841 (J) | chr01 | 25055841 | CT | C | 99.00% | 0.00% | CT -> C | NA |
LOC_Os01g43720.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43740.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.473; most accessible tissue: Zhenshan97 root, score: 88.924 |
| vg0125055851 (J) | chr01 | 25055851 | C | A | 99.50% | 0.00% | C -> A | NA |
LOC_Os01g43720.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g43740.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.525; most accessible tissue: Zhenshan97 root, score: 88.703 |
| vg0125055855 (J) | chr01 | 25055855 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os01g43720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.799; most accessible tissue: Zhenshan97 root, score: 88.238 |
| vg0125055886 (J) | chr01 | 25055886 | A | T | 96.60% | 0.00% | A -> T | NA |
LOC_Os01g43720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.264; most accessible tissue: Zhenshan97 root, score: 88.474 |
| vg0125055903 (J) | chr01 | 25055903 | C | T | 96.70% | 0.00% | C -> T |
LOC_Os01g43720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.952; most accessible tissue: Zhenshan97 root, score: 89.064 |
|
| vg0125055933 (J) | chr01 | 25055933 | A | ATT | 36.90% | 0.04% | A -> AT,ATT,ATT T,ATTTT,T | NA |
LOC_Os01g43720.1 Alt: AT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43740.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43720.1 Alt: ATT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43740.1 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43720.1 Alt: ATTTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43740.1 Alt: ATTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43720.1 Alt: ATTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43740.1 Alt: ATTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 72.306; most accessible tissue: Zhenshan97 root, score: 88.778 |
| vg0125055941 (J) | chr01 | 25055941 | TAA | TTAAA | 88.00% | 0.00% | TAA -> TTAAA,TAAA A,TTTAAA,T TTAAAA,TTT TAAA,T | NA |
LOC_Os01g43720.1 Alt: TTTAAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43740.1 Alt: TTTAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43720.1 Alt: TTAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43740.1 Alt: TTAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43720.1 Alt: TAAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43740.1 Alt: TAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43720.1 Alt: TTTAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43740.1 Alt: TTTAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43720.1 Alt: TTTTAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g43740.1 Alt: TTTTAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.798; most accessible tissue: Zhenshan97 root, score: 89.337 |
| vg0125055942 (J) | chr01 | 25055942 | T | A | 45.70% | 6.98% | A -> T | NA |
LOC_Os01g43720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 73.902; most accessible tissue: Zhenshan97 root, score: 89.337 |
| vg0125055943 (J) | chr01 | 25055943 | A | ATTTTT | 99.60% | 0.00% | A -> ATTTTT | NA |
LOC_Os01g43720.1 Alt: ATTTTT| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g43740.1 Alt: ATTTTT| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 73.902; most accessible tissue: Zhenshan97 root, score: 89.337 |
| vg0125056016 (J) | chr01 | 25056016 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os01g43720.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g43740.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 76.860; most accessible tissue: Zhenshan97 root, score: 90.251 |
| vg0125056092 (J) | chr01 | 25056092 | T | G | 99.70% | 0.00% | T -> G | NA |
LOC_Os01g43720.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g43740.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.285; most accessible tissue: Zhenshan97 root, score: 90.632 |
| vg0125056108 (J) | chr01 | 25056108 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os01g43720.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g43740.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.906; most accessible tissue: Zhenshan97 root, score: 90.835 |
| vg0125056142 (J) | chr01 | 25056142 | T | G | 54.80% | 0.00% | G -> T | NA |
LOC_Os01g43720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.957; most accessible tissue: Zhenshan97 root, score: 90.835 |
| vg0125056493 (J) | chr01 | 25056493 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os01g43740.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g43720.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.302; most accessible tissue: Callus, score: 90.679 |
| vg0125056516 (J) | chr01 | 25056516 | A | G | 97.90% | 0.00% | A -> G | NA |
LOC_Os01g43740.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43720.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.917; most accessible tissue: Callus, score: 90.679 |
| vg0125056547 (J) | chr01 | 25056547 | CG | C | 75.70% | 0.00% | C -> CG | NA |
LOC_Os01g43720.1 Alt: CG| frameshift_variant&splice_region_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 71.602; most accessible tissue: Callus, score: 90.679 |
| vg0125056654 (J) | chr01 | 25056654 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os01g43720.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.437; most accessible tissue: Zhenshan97 root, score: 83.426 |
| vg0125056744 (J) | chr01 | 25056744 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os01g43720.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 71.147; most accessible tissue: Callus, score: 92.008 |
| vg0125056763 (J) | chr01 | 25056763 | C | A | 95.90% | 0.00% | C -> A | NA |
LOC_Os01g43720.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 69.593; most accessible tissue: Callus, score: 92.008 |
| vg0125056931 (J) | chr01 | 25056931 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os01g43720.1 Alt: T| missense_variant&splice_region_variant MODERATE(snpEff)
LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 63.033; most accessible tissue: Callus, score: 90.941 |
| vg0125056945 (J) | chr01 | 25056945 | C | T | 96.70% | 0.00% | C -> T |
LOC_Os01g43740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g43720.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.496; most accessible tissue: Callus, score: 90.941 |
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