23 variations found. LOC_Os10g09890 (hypothetical protein), ranging from 5,360,740 bp to 5,361,286 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1005360752 (J) | chr10 | 5360752 | G | A | 63.10% | 24.90% | G -> A | NA |
LOC_Os10g09890.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 47.211; most accessible tissue: Zhenshan97 panicle, score: 81.135 |
| vg1005360762 (J) | chr10 | 5360762 | G | A | 64.40% | 24.61% | G -> A |
LOC_Os10g09890.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 47.265; most accessible tissue: Zhenshan97 panicle, score: 80.486 |
|
| vg1005360774 (J) | chr10 | 5360774 | G | A | 64.30% | 24.59% | G -> A | NA |
LOC_Os10g09890.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 46.772; most accessible tissue: Zhenshan97 panicle, score: 80.486 |
| vg1005360786 (J) | chr10 | 5360786 | A | C | 37.20% | 21.56% | C -> A | NA |
LOC_Os10g09890.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 46.287; most accessible tissue: Zhenshan97 panicle, score: 80.486 |
| vg1005360804 (J) | chr10 | 5360804 | G | A | 63.40% | 23.89% | G -> A | NA |
LOC_Os10g09890.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 44.272; most accessible tissue: Zhenshan97 panicle, score: 75.670 |
| vg1005360805 (J) | chr10 | 5360805 | C | G | 63.40% | 23.99% | C -> G | NA |
LOC_Os10g09890.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 43.931; most accessible tissue: Zhenshan97 panicle, score: 75.670 |
| vg1005360811 (J) | chr10 | 5360811 | G | A | 86.30% | 13.33% | G -> A | NA |
LOC_Os10g09890.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 43.734; most accessible tissue: Zhenshan97 panicle, score: 74.671 |
| vg1005360837 (J) | chr10 | 5360837 | G | T | 84.00% | 14.07% | G -> T | NA |
LOC_Os10g09890.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 40.585; most accessible tissue: Zhenshan97 panicle, score: 73.605 |
| vg1005360852 (J) | chr10 | 5360852 | C | T | 77.80% | 18.85% | C -> T | NA |
LOC_Os10g09890.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 40.169; most accessible tissue: Zhenshan97 panicle, score: 72.468 |
| vg1005360874 (J) | chr10 | 5360874 | G | A | 78.50% | 19.11% | G -> A | NA |
LOC_Os10g09890.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 37.813; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg1005360883 (J) | chr10 | 5360883 | C | T | 78.80% | 18.94% | C -> T | NA |
LOC_Os10g09890.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 37.727; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg1005360920 (J) | chr10 | 5360920 | A | G | 77.20% | 19.32% | A -> G | NA |
LOC_Os10g09890.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 34.269; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg1005360963 (J) | chr10 | 5360963 | C | T | 76.70% | 18.28% | C -> T | NA |
LOC_Os10g09910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g09900.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g09890.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 30.501; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 |
| vg1005360971 (J) | chr10 | 5360971 | G | A | 76.60% | 15.02% | G -> A | NA |
LOC_Os10g09910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g09900.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g09890.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 30.267; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 |
| vg1005360994 (J) | chr10 | 5360994 | G | A | 86.40% | 13.25% | G -> A | NA |
LOC_Os10g09910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g09900.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g09890.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 27.820; most accessible tissue: Zhenshan97 flag leaf, score: 56.010 |
| vg1005361002 (J) | chr10 | 5361002 | A | C | 86.20% | 13.25% | A -> C | NA |
LOC_Os10g09910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g09900.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g09890.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 27.991; most accessible tissue: Zhenshan97 flag leaf, score: 56.010 |
| vg1005361003 (J) | chr10 | 5361003 | G | C | 71.30% | 13.94% | G -> C | NA |
LOC_Os10g09910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g09900.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g09890.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 28.207; most accessible tissue: Zhenshan97 flag leaf, score: 56.722 |
| vg1005361035 (J) | chr10 | 5361035 | T | C | 85.90% | 13.12% | T -> C | NA |
LOC_Os10g09910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g09900.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g09890.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 26.531; most accessible tissue: Zhenshan97 flag leaf, score: 56.722 |
| vg1005361072 (J) | chr10 | 5361072 | G | A | 86.20% | 13.18% | G -> A | NA |
LOC_Os10g09890.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 24.078; most accessible tissue: Zhenshan97 flag leaf, score: 56.722 |
| vg1005361086 (J) | chr10 | 5361086 | C | T | 85.60% | 13.33% | C -> T | NA |
LOC_Os10g09890.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.810; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 |
| vg1005361097 (J) | chr10 | 5361097 | G | A | 67.90% | 15.32% | G -> A |
mr1317 (Ind_All); LR P-value: 1.56E-07;
mr1855 (Ind_All); LR P-value: 4.60E-08; mr1914 (Ind_All); LR P-value: 1.18E-06; mr1317_2 (Ind_All); LR P-value: 1.64E-07; mr1587_2 (Ind_All); LR P-value: 4.68E-06; mr1792_2 (Ind_All); LR P-value: 3.64E-06; mr1855_2 (Ind_All); LR P-value: 2.60E-12; mr1897_2 (Ind_All); LR P-value: 4.89E-07; mr1914_2 (Ind_All); LR P-value: 6.57E-12; mr1927_2 (Ind_All); LR P-value: 1.79E-08 |
LOC_Os10g09890.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 20.981; most accessible tissue: Zhenshan97 flag leaf, score: 50.663 |
| vg1005361163 (J) | chr10 | 5361163 | G | A | 75.40% | 19.38% | G -> A | NA |
LOC_Os10g09890.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 18.978; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 |
| vg1005361285 (J) | chr10 | 5361285 | G | A | 75.10% | 20.00% | G -> A | NA |
LOC_Os10g09890.1 Alt: A| splice_region_variant&stop_retained_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g09890.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.529; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 |