195 variations found. Os11g0205900/LOC_Os11g09970 (OsFBX411 - F-box domain containing protein; expressed), ranging from 5,342,460 bp to 5,345,614 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os11g09970 | OsFBX411 - F-box domain containing protein, expressed; RAP ID: Os11g0205900; MSU ID: LOC_Os11g09970 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105342476 (J) | chr11 | 5342476 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os11g09970.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.743; most accessible tissue: Callus, score: 86.836 |
| vg1105342519 (J) | chr11 | 5342519 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os11g09970.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.033; most accessible tissue: Callus, score: 86.836 |
| vg1105342527 (J) | chr11 | 5342527 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os11g09970.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.360; most accessible tissue: Callus, score: 86.836 |
| vg1105342548 (J) | chr11 | 5342548 | T | TACTTAC AA | 99.70% | 0.00% | T -> TACTTACAA | NA |
LOC_Os11g09970.1 Alt: TACTTACAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: TACTTACAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.067; most accessible tissue: Callus, score: 86.836 |
| vg1105342594 (J) | chr11 | 5342594 | G | A | 90.10% | 0.00% | G -> A | NA |
LOC_Os11g09970.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.450; most accessible tissue: Zhenshan97 root, score: 77.733 |
| vg1105342599 (J) | chr11 | 5342599 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os11g09970.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.747; most accessible tissue: Zhenshan97 root, score: 77.733 |
| vg1105342622 (J) | chr11 | 5342622 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os11g09970.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.420; most accessible tissue: Zhenshan97 root, score: 78.040 |
| vg1105342634 (J) | chr11 | 5342634 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os11g09970.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.029; most accessible tissue: Zhenshan97 root, score: 78.340 |
| vg1105342636 (J) | chr11 | 5342636 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os11g09970.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.029; most accessible tissue: Zhenshan97 root, score: 78.340 |
| vg1105342651 (J) | chr11 | 5342651 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os11g09970.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.466; most accessible tissue: Zhenshan97 root, score: 79.185 |
| vg1105342683 (J) | chr11 | 5342683 | T | A | 76.40% | 0.00% | T -> A |
LOC_Os11g09970.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.283; most accessible tissue: Callus, score: 85.918 |
|
| vg1105342776 (J) | chr11 | 5342776 | T | C | 99.50% | 0.00% | T -> C | NA |
LOC_Os11g09970.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.955; most accessible tissue: Callus, score: 85.918 |
| vg1105342781 (J) | chr11 | 5342781 | T | C | 76.40% | 0.00% | T -> C |
Awn_length (Ind_All); LR P-value: 9.52E-06;
mr1097_2 (All); LR P-value: 9.14E-12; mr1624_2 (Ind_All); LR P-value: 3.30E-06; mr1681_2 (All); LR P-value: 4.73E-08; mr1723_2 (Ind_All); LR P-value: 2.10E-08 |
LOC_Os11g09970.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.149; most accessible tissue: Callus, score: 85.918 |
| vg1105342789 (J) | chr11 | 5342789 | T | C | 82.90% | 0.00% | C -> T | NA |
LOC_Os11g09970.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.667; most accessible tissue: Callus, score: 85.918 |
| vg1105342797 (J) | chr11 | 5342797 | G | A | 82.90% | 0.00% | A -> G | NA |
LOC_Os11g09970.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.027; most accessible tissue: Callus, score: 85.918 |
| vg1105342851 (J) | chr11 | 5342851 | A | T | 82.70% | 0.00% | T -> A | NA |
LOC_Os11g09970.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.788; most accessible tissue: Zhenshan97 root, score: 72.671 |
| vg1105342898 (J) | chr11 | 5342898 | C | G | 99.70% | 0.00% | C -> G | NA |
LOC_Os11g09970.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.240; most accessible tissue: Zhenshan97 root, score: 68.289 |
| vg1105342918 (J) | chr11 | 5342918 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os11g09970.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.186; most accessible tissue: Zhenshan97 root, score: 66.982 |
| vg1105342939 (J) | chr11 | 5342939 | T | TC | 99.70% | 0.00% | T -> TC | NA |
LOC_Os11g09970.1 Alt: TC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 52.273; most accessible tissue: Callus, score: 80.414 |
| vg1105342940 (J) | chr11 | 5342940 | T | TTCATCT TCATCCT CATC | 99.70% | 0.00% | T -> TTCATCTTCA TCCTCATC,T TCATCTCCAT CCTCATC | NA |
LOC_Os11g09970.1 Alt: TTCATCTTCATCCTCATC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g09970.1 Alt: TTCATCTCCATCCTCATC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 52.273; most accessible tissue: Callus, score: 80.414 |
| vg1105342941 (J) | chr11 | 5342941 | G | C | 99.70% | 0.00% | G -> C | NA |
LOC_Os11g09970.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 52.273; most accessible tissue: Callus, score: 80.414 |
| vg1105342952 (J) | chr11 | 5342952 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os11g09970.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 51.858; most accessible tissue: Callus, score: 80.414 |
| vg1105342961 (J) | chr11 | 5342961 | G | C | 82.80% | 0.00% | C -> G | NA |
LOC_Os11g09970.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 52.154; most accessible tissue: Callus, score: 80.414 |
| vg1105342963 (J) | chr11 | 5342963 | TA | T | 99.70% | 0.00% | TA -> T | NA |
LOC_Os11g09970.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 52.648; most accessible tissue: Callus, score: 80.414 |
| vg1105342974 (J) | chr11 | 5342974 | A | G | 83.20% | 0.00% | G -> A | NA |
LOC_Os11g09970.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 52.958; most accessible tissue: Callus, score: 80.414 |
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