Search for Variation by Gene:

Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Variations Type:

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Search Results:

54 variations found. LOC_Os12g30780 (retrotransposon protein; putative; unclassified; expressed), ranging from 18,480,206 bp to 18,481,536 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
vg1218480219 (J) chr12 18480219 T C 13.10% 74.57% T -> C
mr1310 (All); LMM P-value: 9.03E-06;
mr1310 (Jap_All); LR P-value: 5.12E-07;
mr1959 (All); LR P-value: 2.23E-09;
mr1310_2 (Jap_All); LR P-value: 4.85E-08;
mr1959_2 (All); LR P-value: 1.45E-15;
mr1959_2 (Jap_All); LR P-value: 3.82E-07
LOC_Os12g30780.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g30780.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.282; most accessible tissue: Callus, score: 21.903
vg1218480220 (J) chr12 18480220 G A 16.80% 72.45% G -> A NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 10.282; most accessible tissue: Callus, score: 21.903
vg1218480248 (J) chr12 18480248 C T 30.00% 64.33% C -> T NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 10.390; most accessible tissue: Callus, score: 21.903
vg1218480317 (J) chr12 18480317 G A 13.30% 84.49% G -> A NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 8.523; most accessible tissue: Callus, score: 21.903
vg1218480372 (J) chr12 18480372 G A 31.20% 52.35% G -> A NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 7.164; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480412 (J) chr12 18480412 G A 37.20% 50.02% G -> A NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 6.918; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480424 (J) chr12 18480424 C T 36.70% 49.94% C -> T NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 6.828; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480449 (J) chr12 18480449 C T 21.30% 56.71% C -> T NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 6.758; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480505 (J) chr12 18480505 C T 19.80% 72.81% C -> T NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 6.758; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480537 (J) chr12 18480537 G A 16.10% 72.05% G -> A NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g30780.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 6.845; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480538 (J) chr12 18480538 T A 13.00% 77.57% T -> A NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 6.845; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480563 (J) chr12 18480563 G T 22.20% 66.63% G -> T NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 6.845; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480566 (J) chr12 18480566 G A 31.60% 62.95% G -> A NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 6.845; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480603 (J) chr12 18480603 G A 33.80% 61.38% G -> A NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 6.277; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480608 (J) chr12 18480608 C T 31.10% 63.46% C -> T NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 6.277; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480619 (J) chr12 18480619 A G 29.90% 62.63% A -> G NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 6.277; most accessible tissue: Minghui63 young leaf, score: 11.521
vg1218480675 (J) chr12 18480675 C T 13.20% 81.93% C -> T NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 7.299; most accessible tissue: Callus, score: 17.876
vg1218480729 (J) chr12 18480729 C T 37.80% 49.24% C -> T NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 6.845; most accessible tissue: Callus, score: 17.876
vg1218480780 (J) chr12 18480780 C T 33.70% 52.58% C -> T NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 6.619; most accessible tissue: Callus, score: 17.876
vg1218480799 (J) chr12 18480799 T C 13.80% 80.32% T -> C NA
LOC_Os12g30780.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.619; most accessible tissue: Callus, score: 17.876
vg1218480868 (J) chr12 18480868 G A 13.30% 82.35% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 6.762; most accessible tissue: Callus, score: 17.698
vg1218480894 (J) chr12 18480894 A C 12.90% 83.45% A -> C NA
LOC_Os12g30770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 8.410; most accessible tissue: Callus, score: 17.698
vg1218480907 (J) chr12 18480907 T C 12.80% 86.16% T -> C NA
LOC_Os12g30770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 10.786; most accessible tissue: Minghui63 panicle, score: 20.733
vg1218480937 (J) chr12 18480937 G A 18.60% 69.11% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 13.265; most accessible tissue: Minghui63 panicle, score: 29.741
vg1218480994 (J) chr12 18480994 T C 12.80% 85.15% T -> C NA
LOC_Os12g30770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 25.323; most accessible tissue: Minghui63 panicle, score: 42.799
vg1218480995 (J) chr12 18480995 G A 12.90% 85.63% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 25.323; most accessible tissue: Minghui63 panicle, score: 42.799
vg1218481011 (J) chr12 18481011 G A 12.70% 86.25% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 26.936; most accessible tissue: Minghui63 panicle, score: 53.770
vg1218481138 (J) chr12 18481138 G T 34.80% 57.81% G -> T,C NA
LOC_Os12g30770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 34.338; most accessible tissue: Minghui63 young leaf, score: 60.103
vg1218481140 (J) chr12 18481140 C G 34.90% 57.68% C -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 34.815; most accessible tissue: Minghui63 young leaf, score: 61.887
vg1218481143 (J) chr12 18481143 C T 21.90% 63.56% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 34.845; most accessible tissue: Minghui63 young leaf, score: 61.887
vg1218481154 (J) chr12 18481154 A T 33.50% 59.06% A -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 35.060; most accessible tissue: Minghui63 young leaf, score: 61.887
vg1218481160 (J) chr12 18481160 G T 27.70% 44.29% G -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 35.060; most accessible tissue: Minghui63 young leaf, score: 61.887
vg1218481172 (J) chr12 18481172 G T 36.70% 57.38% G -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 35.180; most accessible tissue: Minghui63 young leaf, score: 61.887
vg1218481201 (J) chr12 18481201 C T 17.90% 74.61% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 36.541; most accessible tissue: Minghui63 young leaf, score: 62.741
vg1218481202 (J) chr12 18481202 G T 17.70% 74.46% G -> T,A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 36.690; most accessible tissue: Minghui63 young leaf, score: 64.378
vg1218481208 (J) chr12 18481208 A G 14.00% 76.60% A -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 36.690; most accessible tissue: Minghui63 young leaf, score: 64.378
vg1218481214 (J) chr12 18481214 G T 16.60% 78.67% G -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 36.690; most accessible tissue: Minghui63 young leaf, score: 64.378
vg1218481219 (J) chr12 18481219 C T 18.00% 73.51% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 36.852; most accessible tissue: Minghui63 young leaf, score: 64.378
vg1218481252 (J) chr12 18481252 C T 16.40% 76.13% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 36.879; most accessible tissue: Minghui63 young leaf, score: 65.161
vg1218481256 (J) chr12 18481256 C T 34.30% 55.90% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 36.879; most accessible tissue: Minghui63 young leaf, score: 65.161
vg1218481261 (J) chr12 18481261 G A 17.30% 75.29% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 36.941; most accessible tissue: Minghui63 young leaf, score: 65.161
vg1218481269 (J) chr12 18481269 T C 13.20% 76.91% T -> C NA
LOC_Os12g30770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 36.941; most accessible tissue: Minghui63 young leaf, score: 65.161
vg1218481270 (J) chr12 18481270 G A 18.20% 73.89% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 36.941; most accessible tissue: Minghui63 young leaf, score: 65.161
vg1218481288 (J) chr12 18481288 G A 32.20% 58.34% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 36.772; most accessible tissue: Minghui63 young leaf, score: 65.161
vg1218481304 (J) chr12 18481304 C T 14.80% 75.39% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 35.824; most accessible tissue: Minghui63 young leaf, score: 64.378
vg1218481382 (J) chr12 18481382 T C 13.20% 83.47% T -> C NA
LOC_Os12g30770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 25.920; most accessible tissue: Minghui63 young leaf, score: 44.630
vg1218481384 (J) chr12 18481384 G A 13.50% 82.16% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 25.353; most accessible tissue: Minghui63 young leaf, score: 44.630
vg1218481387 (J) chr12 18481387 G A 13.20% 83.62% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 25.353; most accessible tissue: Minghui63 young leaf, score: 44.630
vg1218481396 (J) chr12 18481396 A C 13.10% 83.66% A -> C NA
LOC_Os12g30780.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 23.895; most accessible tissue: Minghui63 young leaf, score: 42.042
vg1218481397 (J) chr12 18481397 A G 13.10% 83.75% A -> G NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 23.468; most accessible tissue: Minghui63 young leaf, score: 38.036
vg1218481404 (J) chr12 18481404 A G 13.10% 83.71% A -> G NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 22.204; most accessible tissue: Minghui63 young leaf, score: 39.381
vg1218481405 (J) chr12 18481405 C G 13.10% 83.58% C -> G NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 22.047; most accessible tissue: Minghui63 young leaf, score: 39.381
vg1218481413 (J) chr12 18481413 A G 13.10% 84.49% A -> G NA
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 22.104; most accessible tissue: Minghui63 young leaf, score: 39.381
vg1218481506 (J) chr12 18481506 T C 12.70% 84.28% T -> C NA
LOC_Os12g30780.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 20.187; most accessible tissue: Callus, score: 29.312