9 variations found. Os11g0138700/LOC_Os11g04330 (OsFBK24 - F-box domain and kelch repeat containing protein; expressed), ranging from 1,801,183 bp to 1,802,662 bp (including 0 kb upstream and 0 kb downstream of the gene).
Gene ID | Annotation |
---|---|
LOC_Os11g04330 | OsFBK24 - F-box domain and kelch repeat containing protein, expressed; RAP ID: Os11g0138700; MSU ID: LOC_Os11g04330 |
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 |
---|---|---|---|---|---|---|---|---|---|
vg1101801245 (J) | chr11 | 1801245 | C | G | 79.20% | 0.00% | C -> G |
Heading_date (Ind_All); LR P-value: 2.90E-10;
mr1170 (Ind_All); LR P-value: 8.98E-06; mr1598 (Ind_All); LR P-value: 1.46E-06; mr1835 (All); LR P-value: 1.48E-06; mr1904 (All); LR P-value: 9.16E-14; mr1904 (Ind_All); LMM P-value: 8.94E-06; LR P-value: 1.88E-11; mr1024_2 (Ind_All); LR P-value: 5.01E-07; mr1072_2 (Ind_All); LR P-value: 1.93E-07; mr1075_2 (Ind_All); LR P-value: 1.31E-07; mr1077_2 (Ind_All); LR P-value: 2.96E-08; mr1265_2 (All); LR P-value: 1.69E-06; mr1528_2 (All); LR P-value: 2.32E-07; mr1531_2 (Ind_All); LR P-value: 1.02E-06; mr1558_2 (Ind_All); LR P-value: 9.53E-07; mr1565_2 (Ind_All); LR P-value: 6.04E-12; mr1598_2 (Ind_All); LR P-value: 4.83E-10; mr1659_2 (Ind_All); LR P-value: 1.04E-06; mr1835_2 (Ind_All); LR P-value: 5.27E-06; mr1861_2 (Ind_All); LR P-value: 2.24E-10; mr1904_2 (Ind_All); LR P-value: 6.58E-08; mr1962_2 (Ind_All); LR P-value: 9.57E-09 |
LOC_Os11g04330.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g04310.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04320.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.933; most accessible tissue: Zhenshan97 panicle, score: 96.414 |
vg1101801324 (J) | chr11 | 1801324 | A | C | 98.80% | 0.11% | A -> C | NA |
LOC_Os11g04330.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g04330.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 89.143; most accessible tissue: Zhenshan97 panicle, score: 96.335 |
vg1101801390 (J) | chr11 | 1801390 | T | C | 65.60% | 0.00% | C -> T | NA |
LOC_Os11g04330.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 82.938; most accessible tissue: Zhenshan97 panicle, score: 95.438 |
vg1101801520 (J) | chr11 | 1801520 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os11g04330.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.133; most accessible tissue: Zhenshan97 panicle, score: 94.740 |
vg1101801545 (J) | chr11 | 1801545 | G | T | 99.30% | 0.00% | G -> T | NA |
LOC_Os11g04330.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g04310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g04320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g04340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.547; most accessible tissue: Zhenshan97 panicle, score: 94.668 |
vg1101801666 (J) | chr11 | 1801666 | C | T | 79.10% | 0.00% | C -> T |
Heading_date (Ind_All); LR P-value: 2.90E-10;
mr1170 (Ind_All); LR P-value: 8.98E-06; mr1598 (Ind_All); LR P-value: 1.46E-06; mr1681 (All); LR P-value: 3.17E-06; mr1835 (All); LR P-value: 1.73E-06; mr1904 (All); LR P-value: 1.11E-13; mr1904 (Ind_All); LMM P-value: 8.94E-06; LR P-value: 1.88E-11; mr1024_2 (Ind_All); LR P-value: 5.01E-07; mr1072_2 (Ind_All); LR P-value: 1.93E-07; mr1075_2 (Ind_All); LR P-value: 1.31E-07; mr1077_2 (Ind_All); LR P-value: 2.96E-08; mr1265_2 (All); LR P-value: 1.93E-06; mr1528_2 (All); LR P-value: 7.07E-08; mr1531_2 (Ind_All); LR P-value: 1.02E-06; mr1558_2 (Ind_All); LR P-value: 9.53E-07; mr1565_2 (Ind_All); LR P-value: 6.04E-12; mr1598_2 (Ind_All); LR P-value: 4.83E-10; mr1659_2 (Ind_All); LR P-value: 1.04E-06; mr1835_2 (Ind_All); LR P-value: 5.27E-06; mr1861_2 (Ind_All); LR P-value: 2.24E-10; mr1904_2 (Ind_All); LR P-value: 6.58E-08; mr1962_2 (Ind_All); LR P-value: 9.57E-09 |
LOC_Os11g04330.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 84.653; most accessible tissue: Zhenshan97 panicle, score: 94.195 |
vg1101802168 (J) | chr11 | 1802168 | C | G | 95.50% | 1.12% | C -> G | NA |
LOC_Os11g04330.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g04330.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 87.898; most accessible tissue: Zhenshan97 root, score: 95.274 |
vg1101802207 (J) | chr11 | 1802207 | C | T | 96.00% | 1.12% | C -> T | NA |
LOC_Os11g04330.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g04330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 89.221; most accessible tissue: Zhenshan97 root, score: 95.258 |
vg1101802247 (J) | chr11 | 1802247 | T | G | 95.90% | 1.12% | T -> G | NA |
LOC_Os11g04330.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g04330.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 89.015; most accessible tissue: Zhenshan97 root, score: 95.226 |