13 variations found. LOC_Os11g05290 (stress responsive A%2FB Barrel domain containing protein; expressed), ranging from 2,343,615 bp to 2,344,713 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1102343694 (J) | chr11 | 2343694 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os11g05290.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g05280.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05300.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.076; most accessible tissue: Zhenshan97 panicle, score: 88.350 |
| vg1102343860 (J) | chr11 | 2343860 | T | C | 64.30% | 0.00% | C -> T |
mr1238 (All); LR P-value: 8.98E-26;
mr1448 (All); LR P-value: 6.78E-31; mr1751 (All); LR P-value: 2.55E-11; mr1806 (All); LR P-value: 4.95E-09; mr1191_2 (All); LR P-value: 3.94E-13; mr1553_2 (All); LR P-value: 1.17E-12; mr1767_2 (All); LR P-value: 6.09E-16; mr1806_2 (All); LR P-value: 5.88E-11; mr1873_2 (All); LR P-value: 5.06E-32; mr1904_2 (All); LR P-value: 4.75E-13; mr1968_2 (All); LR P-value: 2.16E-21 |
LOC_Os11g05290.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g05280.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05300.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.691; most accessible tissue: Zhenshan97 panicle, score: 88.625 |
| vg1102343908 (J) | chr11 | 2343908 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os11g05290.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os11g05280.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g05300.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.813; most accessible tissue: Zhenshan97 flower, score: 87.488 |
| vg1102343943 (J) | chr11 | 2343943 | C | A | 64.50% | 0.00% | A -> C |
mr1191 (All); LR P-value: 1.63E-09;
mr1238 (All); LR P-value: 1.67E-26; mr1751 (All); LR P-value: 2.64E-11; mr1806 (All); LR P-value: 8.96E-09; mr1191_2 (All); LR P-value: 2.97E-13; mr1216_2 (All); LR P-value: 4.19E-11; mr1553_2 (All); LR P-value: 2.81E-12; mr1767_2 (All); LR P-value: 9.14E-15; mr1904_2 (All); LR P-value: 1.96E-12; mr1968_2 (All); LR P-value: 8.18E-21 |
LOC_Os11g05290.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.546; most accessible tissue: Zhenshan97 flower, score: 85.963 |
| vg1102344026 (J) | chr11 | 2344026 | C | T | 96.60% | 0.00% | C -> T | NA |
LOC_Os11g05290.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 77.787; most accessible tissue: Zhenshan97 flower, score: 84.874 |
| vg1102344049 (J) | chr11 | 2344049 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os11g05290.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.332; most accessible tissue: Zhenshan97 flower, score: 84.783 |
| vg1102344133 (J) | chr11 | 2344133 | A | AAAGAGA TT | 60.30% | 0.00% | AAAGAGATT -> A | NA |
LOC_Os11g05280.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g05300.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.873; most accessible tissue: Zhenshan97 panicle, score: 83.904 |
| vg1102344378 (J) | chr11 | 2344378 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os11g05280.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os11g05300.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g05290.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.632; most accessible tissue: Zhenshan97 panicle, score: 86.788 |
| vg1102344383 (J) | chr11 | 2344383 | T | A | 96.60% | 0.00% | T -> A | NA |
LOC_Os11g05280.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g05300.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 |
| vg1102344384 (J) | chr11 | 2344384 | A | T | 99.70% | 0.00% | A -> T | NA |
LOC_Os11g05280.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g05300.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.602; most accessible tissue: Zhenshan97 panicle, score: 86.788 |
| vg1102344460 (J) | chr11 | 2344460 | A | G | 99.60% | 0.00% | A -> G | NA |
LOC_Os11g05290.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os11g05280.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05300.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.851; most accessible tissue: Zhenshan97 panicle, score: 90.061 |
| vg1102344622 (J) | chr11 | 2344622 | GCT | G | 83.60% | 0.00% | GCT -> G | NA |
LOC_Os11g05290.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g05280.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05300.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.221; most accessible tissue: Zhenshan97 panicle, score: 94.811 |
| vg1102344709 (J) | chr11 | 2344709 | AGAGTGA GTGAGT | AGAGTGA GTGAGTG AGT | 42.80% | 0.02% | AGAGTGAGTG AGT -> AGAGTGAGTG AGTGAGT,AG AGTGAGT,AG AGTGAGTGAG TGAGTGAGT, A,AGAGT | NA |
LOC_Os11g05290.1 Alt: AGAGTGAGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g05280.1 Alt: AGAGTGAGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05300.1 Alt: AGAGTGAGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290-LOC_Os11g05300 Alt: AGAGTGAGT| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05280.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05300.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290-LOC_Os11g05300 Alt: A| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290.1 Alt: A| non_coding_transcript_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os11g05290.1 Alt: AGAGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05280.1 Alt: AGAGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05300.1 Alt: AGAGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290-LOC_Os11g05300 Alt: AGAGT| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290.1 Alt: AGAGTGAGTGAGTGAGTGAGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05280.1 Alt: AGAGTGAGTGAGTGAGTGAGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05300.1 Alt: AGAGTGAGTGAGTGAGTGAGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290-LOC_Os11g05300 Alt: AGAGTGAGTGAGTGAGTGAGT| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290.1 Alt: AGAGTGAGTGAGTGAGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05280.1 Alt: AGAGTGAGTGAGTGAGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05300.1 Alt: AGAGTGAGTGAGTGAGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g05290-LOC_Os11g05300 Alt: AGAGTGAGTGAGTGAGT| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.925; most accessible tissue: Zhenshan97 panicle, score: 96.173 |