15 variations found. LOC_Os11g23950 (retrotransposon protein; putative; unclassified), ranging from 13,567,896 bp to 13,568,109 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1113567908 (J) | chr11 | 13567908 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os11g23950.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os11g23940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 32.540; most accessible tissue: Minghui63 flag leaf, score: 48.324 |
| vg1113567918 (J) | chr11 | 13567918 | A | T | 99.50% | 0.00% | A -> T | NA |
LOC_Os11g23950.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 32.624; most accessible tissue: Minghui63 flag leaf, score: 48.324 |
| vg1113567937 (J) | chr11 | 13567937 | TGGCGCC AACACCG ATGCCCC ATCAATT GGCTAAC TCGTCAG TCTGTTA CCC | T | 76.20% | 0.00% | TGGCGCCAAC ACCGATGCCC CATCAATTGG CTAACTCGTC AGTCTGTTAC CC -> T | NA |
LOC_Os11g23950.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 32.581; most accessible tissue: Minghui63 flag leaf, score: 45.195 |
| vg1113567958 (J) | chr11 | 13567958 | A | T | 57.40% | 0.00% | A -> T |
LOC_Os11g23950.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 32.091; most accessible tissue: Minghui63 flag leaf, score: 43.614 |
|
| vg1113567982 (J) | chr11 | 13567982 | G | A | 99.10% | 0.00% | G -> A | NA |
LOC_Os11g23950.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 32.730; most accessible tissue: Minghui63 flag leaf, score: 45.195 |
| vg1113567989 (J) | chr11 | 13567989 | G | A | 98.30% | 0.00% | G -> A | NA |
LOC_Os11g23950.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 33.332; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 |
| vg1113567999 (J) | chr11 | 13567999 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os11g23950.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g23950.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 33.735; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 |
| vg1113568000 (J) | chr11 | 13568000 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os11g23950.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 33.735; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 |
| vg1113568005 (J) | chr11 | 13568005 | G | C | 88.00% | 0.00% | G -> C |
mr1059 (Ind_All); LR P-value: 3.36E-09;
mr1143 (Ind_All); LR P-value: 7.91E-12; mr1167 (Ind_All); LR P-value: 8.76E-11; mr1399 (Ind_All); LR P-value: 4.56E-07; mr1502 (Ind_All); LR P-value: 9.79E-06; mr1535 (Ind_All); LR P-value: 9.89E-10; mr1609 (Ind_All); LR P-value: 2.85E-06; mr1675 (Ind_All); LR P-value: 2.72E-10; mr1726 (Ind_All); LR P-value: 1.39E-08; mr1829 (Ind_All); LR P-value: 3.37E-09; mr1902 (Ind_All); LR P-value: 2.39E-08; mr1950 (Ind_All); LR P-value: 7.18E-08; mr1969 (Ind_All); LR P-value: 1.18E-11; mr1995 (Ind_All); LR P-value: 4.13E-12; mr1154_2 (Ind_All); LR P-value: 1.53E-06; mr1167_2 (Ind_All); LR P-value: 6.76E-09; mr1458_2 (Ind_All); LR P-value: 1.60E-07; mr1959_2 (Ind_All); LR P-value: 9.40E-06 |
LOC_Os11g23950.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 33.735; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 |
| vg1113568064 (J) | chr11 | 13568064 | GGACATA | G | 97.20% | 0.00% | GGACATA -> G | NA |
LOC_Os11g23950.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 32.036; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 |
| vg1113568070 (J) | chr11 | 13568070 | G | A | 63.60% | 0.00% | A -> G | NA |
LOC_Os11g23950.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 31.341; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 |
| vg1113568071 (J) | chr11 | 13568071 | G | A | 96.80% | 2.35% | G -> A | NA |
LOC_Os11g23950.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g23950.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 31.341; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 |
| vg1113568104 (J) | chr11 | 13568104 | G | C | 66.30% | 0.00% | C -> G,T | NA |
LOC_Os11g23950.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g23950.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 28.322; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 |
| vg1113568107 (J) | chr11 | 13568107 | T | C | 99.50% | 0.00% | T -> C | NA |
LOC_Os11g23950.1 Alt: C| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar)
The average chromatin accessibility score: 28.107; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 |
| STR1113568057 (J) | chr11 | 13568057 | TGGACAT GGACAT | TGGACAT | 92.20% | 0.00% | TGGACATGGA CAT -> TGGACAT | NA |
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