14 variations found. LOC_Os02g02370 (myb-like DNA-binding domain containing protein; putative; expressed), ranging from 789,596 bp to 791,081 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0200789612 (J) | chr02 | 789612 | G | A | 73.60% | 0.00% | G -> A |
LOC_Os02g02370.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.392; most accessible tissue: Zhenshan97 panicle, score: 87.451 |
|
| vg0200789717 (J) | chr02 | 789717 | C | T | 81.90% | 0.00% | C -> T |
mr1070 (All); LR P-value: 2.41E-11;
mr1092 (Jap_All); LR P-value: 1.67E-06; mr1097 (All); LR P-value: 2.52E-10; mr1154 (Jap_All); LR P-value: 6.40E-07; mr1415 (Ind_All); LR P-value: 5.62E-06; mr1502 (All); LR P-value: 7.77E-06; mr1567 (Ind_All); LR P-value: 5.62E-06; mr1596 (All); LR P-value: 3.81E-06; mr1680 (All); LR P-value: 1.54E-07; mr1740 (Jap_All); LR P-value: 6.38E-06; mr1742 (All); LR P-value: 4.35E-06; mr1559_2 (Jap_All); LR P-value: 8.11E-06; mr1928_2 (Ind_All); LR P-value: 6.19E-06 |
LOC_Os02g02370.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.348; most accessible tissue: Callus, score: 88.878 |
| vg0200789738 (J) | chr02 | 789738 | G | A | 81.80% | 0.00% | G -> A |
mr1070 (All); LR P-value: 2.41E-11;
mr1092 (Jap_All); LR P-value: 1.67E-06; mr1097 (All); LR P-value: 2.52E-10; mr1154 (Jap_All); LR P-value: 6.40E-07; mr1415 (Ind_All); LR P-value: 5.62E-06; mr1502 (All); LR P-value: 7.77E-06; mr1567 (Ind_All); LR P-value: 5.62E-06; mr1596 (All); LR P-value: 3.81E-06; mr1680 (All); LR P-value: 1.54E-07; mr1740 (Jap_All); LR P-value: 6.38E-06; mr1742 (All); LR P-value: 4.35E-06; mr1559_2 (Jap_All); LR P-value: 8.11E-06; mr1928_2 (Ind_All); LR P-value: 6.19E-06 |
LOC_Os02g02370.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.512; most accessible tissue: Callus, score: 88.878 |
| vg0200790320 (J) | chr02 | 790320 | G | GT | 40.00% | 14.41% | G -> GT,GTTT,GC TTTTTTTAAA CT | NA |
LOC_Os02g02350.2 Alt: GCTTTTTTTAAACT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g02360.1 Alt: GCTTTTTTTAAACT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02380.1 Alt: GCTTTTTTTAAACT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: GCTTTTTTTAAACT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02350.2 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02360.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02380.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: GT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02350.2 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02360.1 Alt: GTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02380.1 Alt: GTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: GTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 64.566; most accessible tissue: Callus, score: 84.374 |
| vg0200790322 (J) | chr02 | 790322 | T | TA | 69.00% | 1.23% | T -> TA | NA |
LOC_Os02g02350.2 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g02360.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02380.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 64.723; most accessible tissue: Callus, score: 84.374 |
| vg0200790328 (J) | chr02 | 790328 | T | TA | 81.90% | 0.00% | T -> TA,A | NA |
LOC_Os02g02350.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g02360.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02380.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02370.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os02g02350.2 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02360.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02380.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.109; most accessible tissue: Zhenshan97 root, score: 70.636 |
| vg0200790342 (J) | chr02 | 790342 | T | A | 74.10% | 0.04% | T -> A | NA |
LOC_Os02g02350.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g02360.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02380.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 60.271; most accessible tissue: Minghui63 panicle, score: 71.773 |
| vg0200790371 (J) | chr02 | 790371 | C | T | 79.30% | 0.00% | C -> T |
mr1029 (All); LR P-value: 2.96E-06;
mr1092 (Jap_All); LR P-value: 3.95E-06; mr1154 (Jap_All); LR P-value: 1.16E-06; mr1189 (All); LR P-value: 1.84E-06; mr1415 (Ind_All); LR P-value: 5.62E-06; mr1502 (All); LR P-value: 3.93E-07; mr1567 (Ind_All); LR P-value: 5.62E-06; mr1625 (All); LR P-value: 1.56E-06; mr1642 (All); LR P-value: 4.93E-07; mr1680 (All); LR P-value: 1.01E-08; mr1684 (All); LR P-value: 2.38E-06; mr1742 (All); LR P-value: 6.28E-06; mr1796 (All); LR P-value: 8.55E-07; mr1990 (All); LR P-value: 1.23E-06; mr1559_2 (Jap_All); LR P-value: 9.25E-06; mr1928_2 (Ind_All); LR P-value: 6.19E-06 |
LOC_Os02g02350.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g02360.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02380.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.479; most accessible tissue: Zhenshan97 root, score: 74.040 |
| vg0200790720 (J) | chr02 | 790720 | GAA | G | 54.30% | 0.00% | G -> GAA,GA,GAA A | NA |
LOC_Os02g02360.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g02380.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02360.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02380.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02360.1 Alt: GAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02380.1 Alt: GAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: GAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.317; most accessible tissue: Callus, score: 86.638 |
| vg0200790778 (J) | chr02 | 790778 | C | A | 78.50% | 0.00% | A -> C |
LOC_Os02g02360.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g02380.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.345; most accessible tissue: Callus, score: 86.638 |
|
| vg0200790780 (J) | chr02 | 790780 | C | CAAGCTA AGCTTGA ACTAACC CA | 52.80% | 0.00% | CAAGCTAAGC TTGAACTAAC CCA -> C | NA |
LOC_Os02g02360.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g02380.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.379; most accessible tissue: Callus, score: 86.638 |
| vg0200790846 (J) | chr02 | 790846 | A | G | 81.10% | 0.00% | G -> A |
LOC_Os02g02360.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g02380.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.644; most accessible tissue: Zhenshan97 root, score: 81.772 |
|
| vg0200790862 (J) | chr02 | 790862 | G | A | 94.20% | 0.00% | G -> A | NA |
LOC_Os02g02360.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g02380.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g02370.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.919; most accessible tissue: Zhenshan97 root, score: 81.772 |
| STR0200789712 (J) | chr02 | 789712 | TGCTGCT G | TGCTGTT G | 80.20% | 0.00% | TGCTGCTG -> TGCTGTTG | NA |
|