12 variations found. Os10g0537400/LOC_Os10g39210 (heavy metal-associated domain containing protein; expressed), ranging from 20,935,117 bp to 20,935,789 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os10g39210 | heavy metal-associated domain containing protein; RAP ID: Os10g0537400; MSU ID: LOC_Os10g39210 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1020935380 (J) | chr10 | 20935380 | T | C | 53.40% | 0.28% | C -> T |
LOC_Os10g39200.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39220.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39200.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39200.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39200.4 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39210.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 77.605; most accessible tissue: Zhenshan97 root, score: 98.926 |
|
| vg1020935387 (J) | chr10 | 20935387 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os10g39200.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os10g39220.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g39200.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g39200.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g39200.4 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g39210.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.605; most accessible tissue: Zhenshan97 root, score: 98.930 |
| vg1020935399 (J) | chr10 | 20935399 | G | A | 96.60% | 0.00% | G -> A | NA |
LOC_Os10g39200.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39220.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39200.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39200.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39200.4 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39210.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.594; most accessible tissue: Zhenshan97 root, score: 98.932 |
| vg1020935413 (J) | chr10 | 20935413 | G | A | 59.80% | 0.30% | A -> G |
mr1748 (All); LR P-value: 2.64E-06;
mr1829 (Ind_All); LR P-value: 1.45E-08; mr1902 (All); LR P-value: 2.15E-12; mr1050_2 (All); LR P-value: 3.64E-09; mr1348_2 (All); LR P-value: 7.82E-06; mr1349_2 (All); LR P-value: 1.23E-10; mr1829_2 (Ind_All); LR P-value: 5.20E-09; mr1902_2 (Ind_All); LR P-value: 3.35E-09 |
LOC_Os10g39200.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39220.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39200.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39200.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39200.4 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39210.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 77.571; most accessible tissue: Zhenshan97 root, score: 98.951 |
| vg1020935423 (J) | chr10 | 20935423 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os10g39200.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os10g39220.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g39200.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g39200.3 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g39200.4 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g39210.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.575; most accessible tissue: Zhenshan97 root, score: 98.960 |
| vg1020935467 (J) | chr10 | 20935467 | G | A | 96.60% | 0.00% | G -> A | NA |
LOC_Os10g39210.1 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 79.401; most accessible tissue: Zhenshan97 root, score: 98.979 |
| vg1020935498 (J) | chr10 | 20935498 | A | G | 57.50% | 0.30% | G -> A |
mr1133 (All); LR P-value: 2.59E-18;
mr1343 (Ind_All); LR P-value: 8.54E-06; mr1667 (All); LR P-value: 9.75E-12; mr1829 (Ind_All); LR P-value: 1.59E-08; mr1902 (All); LR P-value: 3.23E-12; mr1050_2 (All); LR P-value: 1.11E-09; mr1133_2 (All); LR P-value: 1.95E-15; mr1348_2 (All); LR P-value: 1.93E-06; mr1349_2 (All); LR P-value: 2.98E-11; mr1568_2 (All); LR P-value: 2.06E-07; mr1598_2 (All); LR P-value: 4.36E-33; mr1667_2 (All); LR P-value: 1.85E-10; mr1829_2 (Ind_All); LR P-value: 1.92E-09; mr1902_2 (Ind_All); LR P-value: 8.76E-10 |
LOC_Os10g39210.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g39210.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 79.265; most accessible tissue: Zhenshan97 root, score: 98.843 |
| vg1020935579 (J) | chr10 | 20935579 | C | T | 59.70% | 0.04% | T -> C |
Grain_weight (Jap_All); LR P-value: 9.60E-06;
mr1281 (All); LR P-value: 6.60E-11; mr1748 (All); LR P-value: 1.18E-06; mr1829 (Ind_All); LR P-value: 1.45E-08; mr1902 (All); LR P-value: 9.61E-13; mr1050_2 (All); LR P-value: 4.07E-10; mr1349_2 (All); LR P-value: 1.40E-10; mr1829_2 (Ind_All); LR P-value: 5.20E-09; mr1902_2 (Ind_All); LR P-value: 3.35E-09 |
LOC_Os10g39210.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g39210.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.636; most accessible tissue: Zhenshan97 root, score: 98.419 |
| vg1020935632 (J) | chr10 | 20935632 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os10g39210.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.767; most accessible tissue: Zhenshan97 root, score: 98.519 |
| vg1020935703 (J) | chr10 | 20935703 | C | T | 57.70% | 0.23% | T -> C |
mr1133 (All); LR P-value: 3.06E-19;
mr1343 (Ind_All); LR P-value: 7.60E-06; mr1667 (All); LR P-value: 3.75E-12; mr1829 (Ind_All); LR P-value: 3.08E-08; mr1902 (All); LR P-value: 1.65E-11; mr1050_2 (All); LR P-value: 1.37E-09; mr1133_2 (All); LR P-value: 7.83E-16; mr1348_2 (All); LR P-value: 1.26E-06; mr1349_2 (All); LR P-value: 6.08E-11; mr1568_2 (All); LR P-value: 3.17E-07; mr1598_2 (All); LR P-value: 3.10E-33; mr1667_2 (All); LR P-value: 6.31E-11; mr1829_2 (Ind_All); LR P-value: 3.05E-09; mr1902_2 (Ind_All); LR P-value: 7.97E-10 |
LOC_Os10g39210.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os10g39210.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 79.299; most accessible tissue: Zhenshan97 root, score: 98.172 |
| vg1020935748 (J) | chr10 | 20935748 | C | T | 53.50% | 0.25% | T -> C |
LOC_Os10g39210.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g39210.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.863; most accessible tissue: Zhenshan97 root, score: 97.856 |
|
| vg1020935761 (J) | chr10 | 20935761 | A | G | 99.10% | 0.00% | A -> G | NA |
LOC_Os10g39210.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 78.745; most accessible tissue: Zhenshan97 root, score: 97.778 |