12 variations found. LOC_Os02g13220 (F-box family protein; putative; expressed), ranging from 7,044,616 bp to 7,046,245 bp (including 0 kb upstream and 0 kb downstream of the gene).
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0207044637 (J) | chr02 | 7044637 | A | G | 87.60% | 0.00% | A -> G |
mr1608 (Ind_All); LR P-value: 3.25E-06;
mr1296_2 (All); LR P-value: 2.09E-06; mr1376_2 (Ind_All); LR P-value: 5.28E-06; mr1431_2 (Ind_All); LR P-value: 2.05E-06; mr1611_2 (Ind_All); LR P-value: 2.07E-06; mr1721_2 (Ind_All); LR P-value: 1.68E-06; mr1743_2 (All); LR P-value: 2.07E-06; mr1743_2 (Ind_All); LR P-value: 2.53E-06; mr1756_2 (Ind_All); LR P-value: 7.31E-07; mr1882_2 (All); LR P-value: 3.98E-06 |
LOC_Os02g13220.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13210.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.167; most accessible tissue: Zhenshan97 young leaf, score: 89.226 |
| vg0207045017 (J) | chr02 | 7045017 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os02g13220.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os02g13210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.008; most accessible tissue: Zhenshan97 flag leaf, score: 90.738 |
| vg0207045229 (J) | chr02 | 7045229 | G | C | 60.40% | 0.15% | C -> G |
mr1137 (Jap_All); LR P-value: 3.20E-09;
mr1229 (All); LR P-value: 1.76E-06; mr1486 (Jap_All); LR P-value: 5.11E-10; mr1540 (All); LR P-value: 3.81E-12; mr1608 (Ind_All); LR P-value: 3.75E-06; mr1617 (Jap_All); LR P-value: 4.26E-07; mr1530_2 (Jap_All); LR P-value: 8.56E-10; mr1629_2 (Jap_All); LR P-value: 1.57E-06; mr1743_2 (All); LR P-value: 2.58E-06 |
LOC_Os02g13220.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g13220.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 75.649; most accessible tissue: Zhenshan97 flower, score: 89.174 |
| vg0207045458 (J) | chr02 | 7045458 | C | T | 91.30% | 0.00% | C -> T |
LOC_Os02g13220.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.650; most accessible tissue: Zhenshan97 flower, score: 92.164 |
|
| vg0207045623 (J) | chr02 | 7045623 | G | A | 87.20% | 0.00% | A -> G |
LOC_Os02g13220.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.257; most accessible tissue: Zhenshan97 flower, score: 93.614 |
|
| vg0207045689 (J) | chr02 | 7045689 | CGGCGCG GCG | GGGCGCG GCG | 87.60% | 0.00% | CGGCGCGGCG -> GGGCGCGGCG ,C |
mr1608 (Ind_All); LR P-value: 1.39E-06;
mr1296_2 (All); LR P-value: 2.45E-06; mr1431_2 (Ind_All); LR P-value: 6.82E-06; mr1611_2 (Ind_All); LR P-value: 6.38E-06; mr1721_2 (Ind_All); LR P-value: 4.05E-06; mr1743_2 (All); LR P-value: 9.53E-06; mr1756_2 (Ind_All); LR P-value: 4.36E-07; mr1882_2 (All); LR P-value: 4.87E-06 |
LOC_Os02g13220.1 Alt: GGGCGCGGCG| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g13220.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 86.590; most accessible tissue: Zhenshan97 flower, score: 94.209 |
| vg0207045692 (J) | chr02 | 7045692 | C | A | 56.80% | 0.00% | C -> A,T |
LOC_Os02g13220.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g13220.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 86.595; most accessible tissue: Zhenshan97 flower, score: 94.209 |
|
| vg0207045892 (J) | chr02 | 7045892 | C | T | 91.30% | 0.00% | C -> T |
LOC_Os02g13220.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.063; most accessible tissue: Zhenshan97 flower, score: 96.362 |
|
| vg0207046028 (J) | chr02 | 7046028 | C | T | 91.20% | 0.00% | C -> T | NA |
LOC_Os02g13220.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.029; most accessible tissue: Zhenshan97 flower, score: 96.047 |
| vg0207046035 (J) | chr02 | 7046035 | C | A | 78.70% | 0.00% | A -> C | NA |
LOC_Os02g13220.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.587; most accessible tissue: Zhenshan97 flower, score: 96.588 |
| vg0207046104 (J) | chr02 | 7046104 | G | A | 91.30% | 0.00% | G -> A |
LOC_Os02g13220.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13210.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g13230.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.348; most accessible tissue: Zhenshan97 root, score: 98.012 |
|
| vg0207046168 (J) | chr02 | 7046168 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os02g13220.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g13230.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.526; most accessible tissue: Zhenshan97 root, score: 98.852 |