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Search Results:

14 variations found. LOC_Os03g59910 (transposon protein; putative; unclassified), ranging from 34,098,271 bp to 34,098,677 bp (including 0 kb upstream and 0 kb downstream of the gene).

Variation Map (with Chromatin Accessibility Map/ Non-coding Varation Scores Map) in Searched Region:

The 'big effect' variations are marked out:

ColorExplainDetails
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.

Detailed Variation Information:

Var ID Chrom Position Primary Allele Secondary Allele Primary Allele Frequency DEL Frequency Var GWAS Results Effect
vg0334098308 (J) chr03 34098308 C T 99.60% 0.00% C -> T NA
LOC_Os03g59910.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g59894.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g59920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 51.557; most accessible tissue: Minghui63 panicle, score: 62.157
vg0334098334 (J) chr03 34098334 C T 99.70% 0.00% C -> T NA
LOC_Os03g59910.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g59894.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g59920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 48.119; most accessible tissue: Minghui63 panicle, score: 59.629
vg0334098336 (J) chr03 34098336 A G 53.40% 0.55% G -> A
mr1249 (All); LR P-value: 1.43E-09;
mr1198_2 (All); LR P-value: 1.03E-08;
mr1579_2 (All); LR P-value: 3.62E-14
LOC_Os03g59910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g59910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 49.069; most accessible tissue: Minghui63 panicle, score: 59.629
vg0334098385 (J) chr03 34098385 C T 86.50% 0.00% C -> T,A NA
LOC_Os03g59894.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g59920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g59910.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g59894.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g59920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g59910.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 47.182; most accessible tissue: Minghui63 panicle, score: 59.629
vg0334098434 (J) chr03 34098434 CTTG C 54.00% 0.47% C -> CTTG NA
LOC_Os03g59910.1 Alt: CTTG| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g59894.1 Alt: CTTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g59920.1 Alt: CTTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 51.479; most accessible tissue: Callus, score: 68.635
vg0334098463 (J) chr03 34098463 C T 96.10% 0.00% C -> T NA
LOC_Os03g59910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 50.814; most accessible tissue: Callus, score: 68.635
vg0334098478 (J) chr03 34098478 C T 99.80% 0.00% C -> T NA
LOC_Os03g59910.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g59894.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g59920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 49.521; most accessible tissue: Callus, score: 68.635
vg0334098485 (J) chr03 34098485 C T 99.80% 0.00% C -> T NA
LOC_Os03g59910.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g59894.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g59920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 48.298; most accessible tissue: Callus, score: 68.635
vg0334098510 (J) chr03 34098510 C T 54.10% 0.42% T -> C
mr1098 (Ind_All); LR P-value: 7.82E-06;
mr1249 (All); LMM P-value: 8.51E-06; LR P-value: 8.25E-11;
mr1961 (Ind_All); LR P-value: 5.63E-06;
mr1151_2 (All); LR P-value: 3.43E-12;
mr1198_2 (All); LR P-value: 2.46E-09;
mr1681_2 (All); LR P-value: 1.39E-07
LOC_Os03g59910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os03g59910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 48.675; most accessible tissue: Callus, score: 68.635
vg0334098522 (J) chr03 34098522 T C 53.50% 0.47% C -> T
mr1249 (All); LR P-value: 4.01E-10;
mr1098_2 (Ind_All); LR P-value: 9.09E-06;
mr1198_2 (All); LR P-value: 1.08E-08
LOC_Os03g59910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os03g59910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 47.050; most accessible tissue: Callus, score: 68.635
vg0334098591 (J) chr03 34098591 C T 59.90% 0.36% C -> T NA
LOC_Os03g59910.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os03g59910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 45.694; most accessible tissue: Zhenshan97 young leaf, score: 55.261
vg0334098592 (J) chr03 34098592 G A 99.60% 0.00% G -> A NA
LOC_Os03g59910.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g59894.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g59920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 45.694; most accessible tissue: Zhenshan97 young leaf, score: 55.261
vg0334098669 (J) chr03 34098669 C A 54.10% 0.61% A -> C,T
mr1098 (Ind_All); LR P-value: 3.28E-06;
mr1249 (All); LR P-value: 2.10E-10;
mr1305 (Ind_All); LR P-value: 9.72E-06;
mr1961 (Ind_All); LR P-value: 7.12E-06;
mr1198_2 (All); LR P-value: 2.16E-09;
mr1579_2 (All); LR P-value: 2.90E-14
LOC_Os03g59910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os03g59910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g59910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 44.668; most accessible tissue: Zhenshan97 young leaf, score: 54.618
vg0334098677 (J) chr03 34098677 G A 54.10% 0.61% A -> G
mr1098 (Ind_All); LR P-value: 3.28E-06;
mr1249 (All); LR P-value: 2.10E-10;
mr1305 (Ind_All); LR P-value: 9.72E-06;
mr1961 (Ind_All); LR P-value: 7.12E-06;
mr1198_2 (All); LR P-value: 2.16E-09;
mr1579_2 (All); LR P-value: 2.90E-14
LOC_Os03g59910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g59910.1 Alt: G| splice_region_variant&stop_retained_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 46.168; most accessible tissue: Callus, score: 67.670