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Search Results:

32 variations found. Os12g0420000/LOC_Os12g23150 (4-nitrophenylphosphatase-like; putative; expressed), ranging from 13,095,416 bp to 13,096,603 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os12g23150 4-nitrophenylphosphatase-like, putative, expressed; RAP ID: Os12g0420000; MSU ID: LOC_Os12g23150

Gene Expression Atlas:

The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.

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
vg1213095417 (J) chr12 13095417 T C 88.70% 10.77% T -> C NA
LOC_Os12g23150.1 Alt: C| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar)
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 62.924; most accessible tissue: Minghui63 flower, score: 80.659
vg1213095434 (J) chr12 13095434 A G 88.80% 10.75% A -> G NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 65.526; most accessible tissue: Zhenshan97 young leaf, score: 80.589
vg1213095435 (J) chr12 13095435 A G 88.80% 10.75% A -> G NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 65.526; most accessible tissue: Zhenshan97 young leaf, score: 80.589
vg1213095439 (J) chr12 13095439 A G 71.10% 12.31% G -> A
mr1023 (All); LR P-value: 1.81E-61;
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1079 (All); LR P-value: 4.74E-47;
mr1079 (Jap_All); LR P-value: 7.22E-13;
mr1142 (Jap_All); LR P-value: 4.33E-14;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1182 (All); LR P-value: 2.96E-11;
mr1489 (All); LR P-value: 2.79E-69;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (All); LR P-value: 2.21E-61;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 8.65E-08;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1778 (Jap_All); LR P-value: 3.17E-13;
mr1013_2 (All); LR P-value: 1.41E-16;
mr1023_2 (All); LR P-value: 3.40E-73;
mr1023_2 (Jap_All); LR P-value: 3.13E-16;
mr1031_2 (All); LR P-value: 5.66E-16;
mr1079_2 (All); LR P-value: 2.56E-55;
mr1079_2 (Jap_All); LR P-value: 2.03E-13;
mr1189_2 (Jap_All); LR P-value: 4.69E-08;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1471_2 (All); LR P-value: 3.39E-09;
mr1489_2 (All); LR P-value: 1.32E-78;
mr1489_2 (Jap_All); LR P-value: 5.95E-15;
mr1606_2 (All); LR P-value: 1.06E-07;
mr1607_2 (All); LR P-value: 2.15E-07;
mr1722_2 (All); LR P-value: 1.03E-12;
mr1778_2 (Jap_All); LR P-value: 1.78E-13;
mr1879_2 (All); LR P-value: 2.56E-13;
mr1942_2 (All); LR P-value: 6.84E-10
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 65.768; most accessible tissue: Zhenshan97 young leaf, score: 80.848
vg1213095452 (J) chr12 13095452 C A 88.80% 10.75% C -> A NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 66.426; most accessible tissue: Minghui63 flower, score: 81.266
vg1213095453 (J) chr12 13095453 C A 88.80% 10.75% C -> A NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.366; most accessible tissue: Minghui63 flower, score: 81.118
vg1213095455 (J) chr12 13095455 C T 88.80% 10.77% C -> T NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.366; most accessible tissue: Minghui63 flower, score: 81.118
vg1213095457 (J) chr12 13095457 C A 88.70% 10.81% C -> A NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.366; most accessible tissue: Minghui63 flower, score: 81.118
vg1213095487 (J) chr12 13095487 T C 88.70% 10.85% T -> C NA
LOC_Os12g23150.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 67.517; most accessible tissue: Minghui63 flower, score: 80.659
vg1213095502 (J) chr12 13095502 C A 88.60% 10.94% C -> A NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.162; most accessible tissue: Zhenshan97 young leaf, score: 80.325
vg1213095542 (J) chr12 13095542 T C 88.50% 10.98% T -> C NA
LOC_Os12g23150.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 67.389; most accessible tissue: Zhenshan97 young leaf, score: 80.325
vg1213095546 (J) chr12 13095546 G A 88.60% 10.96% G -> A NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 67.389; most accessible tissue: Zhenshan97 young leaf, score: 80.325
vg1213095548 (J) chr12 13095548 A AAC 88.60% 10.96% A -> AAC NA
LOC_Os12g23150.1 Alt: AAC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 67.891; most accessible tissue: Zhenshan97 young leaf, score: 80.589
vg1213095553 (J) chr12 13095553 A T 88.50% 10.98% A -> T NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 69.437; most accessible tissue: Zhenshan97 young leaf, score: 82.077
vg1213095584 (J) chr12 13095584 C T 88.60% 10.85% C -> T NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 65.296; most accessible tissue: Minghui63 flower, score: 80.339
vg1213095594 (J) chr12 13095594 A G 88.60% 10.85% A -> G NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 64.725; most accessible tissue: Minghui63 flower, score: 78.614
vg1213095595 (J) chr12 13095595 G T 71.00% 12.46% T -> G
mr1023 (All); LR P-value: 8.96E-61;
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1079 (All); LR P-value: 6.39E-46;
mr1079 (Jap_All); LR P-value: 7.22E-13;
mr1142 (Jap_All); LR P-value: 4.33E-14;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1182 (All); LR P-value: 3.32E-11;
mr1308 (All); LR P-value: 7.71E-17;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 5.27E-08;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1778 (Jap_All); LR P-value: 3.17E-13;
mr1013_2 (All); LR P-value: 3.98E-16;
mr1023_2 (All); LR P-value: 1.30E-71;
mr1023_2 (Jap_All); LR P-value: 3.13E-16;
mr1031_2 (All); LR P-value: 3.60E-15;
mr1079_2 (All); LR P-value: 1.59E-54;
mr1079_2 (Jap_All); LR P-value: 2.03E-13;
mr1189_2 (Jap_All); LR P-value: 4.69E-08;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1368_2 (All); LR P-value: 2.71E-32;
mr1471_2 (All); LR P-value: 3.11E-09;
mr1489_2 (All); LR P-value: 1.61E-77;
mr1489_2 (Jap_All); LR P-value: 5.95E-15;
mr1606_2 (All); LR P-value: 1.07E-07;
mr1722_2 (All); LR P-value: 3.41E-12;
mr1778_2 (Jap_All); LR P-value: 1.78E-13;
mr1879_2 (All); LR P-value: 1.19E-12;
mr1942_2 (All); LR P-value: 1.15E-09
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 64.725; most accessible tissue: Minghui63 flower, score: 78.614
vg1213095601 (J) chr12 13095601 T C 88.60% 10.81% T -> C NA
LOC_Os12g23150.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 65.148; most accessible tissue: Minghui63 flower, score: 78.979
vg1213095729 (J) chr12 13095729 G A 65.30% 12.15% G -> A
mr1029 (All); LR P-value: 5.38E-06;
mr1677 (All); LR P-value: 8.04E-07;
mr1796 (All); LR P-value: 1.17E-06
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g23160.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23170.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23150.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 66.136; most accessible tissue: Minghui63 flower, score: 76.594
vg1213095879 (J) chr12 13095879 T C 71.40% 12.12% C -> T
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1079 (Jap_All); LR P-value: 7.22E-13;
mr1142 (Jap_All); LR P-value: 4.33E-14;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1182 (All); LR P-value: 3.09E-11;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 4.70E-08;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1778 (Jap_All); LR P-value: 3.17E-13;
mr1826 (All); LR P-value: 7.17E-06;
mr1013_2 (All); LR P-value: 8.09E-16;
mr1023_2 (Jap_All); LR P-value: 3.13E-16;
mr1031_2 (All); LR P-value: 2.85E-15;
mr1079_2 (Jap_All); LR P-value: 2.03E-13;
mr1189_2 (Jap_All); LR P-value: 4.69E-08;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1471_2 (All); LR P-value: 8.40E-09;
mr1489_2 (Jap_All); LR P-value: 5.95E-15;
mr1722_2 (All); LR P-value: 1.65E-12;
mr1778_2 (Jap_All); LR P-value: 1.78E-13;
mr1879_2 (All); LR P-value: 1.03E-12
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g23160.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23150.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 62.187; most accessible tissue: Minghui63 flower, score: 76.594
vg1213095880 (J) chr12 13095880 A G 88.00% 10.69% A -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g23160.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23170.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23150.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 62.187; most accessible tissue: Minghui63 flower, score: 76.594
vg1213095902 (J) chr12 13095902 T C 71.20% 12.38% C -> T
mr1023 (All); LR P-value: 8.96E-61;
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1079 (All); LR P-value: 6.39E-46;
mr1079 (Jap_All); LR P-value: 7.22E-13;
mr1142 (Jap_All); LR P-value: 4.33E-14;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1182 (All); LR P-value: 3.32E-11;
mr1308 (All); LR P-value: 7.71E-17;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 5.27E-08;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1778 (Jap_All); LR P-value: 3.17E-13;
mr1013_2 (All); LR P-value: 3.98E-16;
mr1023_2 (All); LR P-value: 1.30E-71;
mr1023_2 (Jap_All); LR P-value: 3.13E-16;
mr1031_2 (All); LR P-value: 3.60E-15;
mr1079_2 (All); LR P-value: 1.59E-54;
mr1079_2 (Jap_All); LR P-value: 2.03E-13;
mr1189_2 (Jap_All); LR P-value: 4.69E-08;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1368_2 (All); LR P-value: 2.71E-32;
mr1471_2 (All); LR P-value: 3.11E-09;
mr1489_2 (All); LR P-value: 1.61E-77;
mr1489_2 (Jap_All); LR P-value: 5.95E-15;
mr1606_2 (All); LR P-value: 1.07E-07;
mr1722_2 (All); LR P-value: 3.41E-12;
mr1778_2 (Jap_All); LR P-value: 1.78E-13;
mr1879_2 (All); LR P-value: 1.19E-12;
mr1942_2 (All); LR P-value: 1.15E-09
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g23160.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23150.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 63.061; most accessible tissue: Minghui63 flower, score: 77.644
vg1213095955 (J) chr12 13095955 TAA T 71.20% 12.42% T -> TAA,TGA NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g23160.1 Alt: TGA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23170.1 Alt: TGA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23150.1 Alt: TGA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23160.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23170.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23150.1 Alt: TAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 59.508; most accessible tissue: Minghui63 flower, score: 73.172
vg1213095961 (J) chr12 13095961 C T 79.80% 11.96% C -> T
mr1126_2 (All); LR P-value: 1.41E-06;
mr1166_2 (All); LR P-value: 1.09E-09
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g23160.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23150.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 60.741; most accessible tissue: Minghui63 flag leaf, score: 74.161
vg1213096023 (J) chr12 13096023 G A 87.80% 9.75% G -> A NA
LOC_Os12g23150.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23150.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 60.947; most accessible tissue: Minghui63 flower, score: 74.230
vg1213096467 (J) chr12 13096467 C T 79.50% 12.25% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g23160.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23150.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 80.507; most accessible tissue: Minghui63 flag leaf, score: 92.945
vg1213096474 (J) chr12 13096474 T C 71.30% 12.38% C -> T
mr1023 (All); LR P-value: 1.81E-61;
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1079 (All); LR P-value: 4.74E-47;
mr1079 (Jap_All); LR P-value: 7.22E-13;
mr1142 (Jap_All); LR P-value: 4.33E-14;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1182 (All); LR P-value: 2.96E-11;
mr1489 (All); LR P-value: 2.79E-69;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (All); LR P-value: 2.21E-61;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 8.65E-08;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1778 (Jap_All); LR P-value: 3.17E-13;
mr1013_2 (All); LR P-value: 1.41E-16;
mr1023_2 (All); LR P-value: 3.40E-73;
mr1023_2 (Jap_All); LR P-value: 3.13E-16;
mr1031_2 (All); LR P-value: 5.66E-16;
mr1079_2 (All); LR P-value: 2.56E-55;
mr1079_2 (Jap_All); LR P-value: 2.03E-13;
mr1189_2 (Jap_All); LR P-value: 4.69E-08;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1471_2 (All); LR P-value: 3.39E-09;
mr1489_2 (All); LR P-value: 1.32E-78;
mr1489_2 (Jap_All); LR P-value: 5.95E-15;
mr1606_2 (All); LR P-value: 1.06E-07;
mr1607_2 (All); LR P-value: 2.15E-07;
mr1722_2 (All); LR P-value: 1.03E-12;
mr1778_2 (Jap_All); LR P-value: 1.78E-13;
mr1879_2 (All); LR P-value: 2.56E-13;
mr1942_2 (All); LR P-value: 6.84E-10
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g23160.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23150.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 80.681; most accessible tissue: Minghui63 flag leaf, score: 92.945
vg1213096478 (J) chr12 13096478 C A 80.40% 12.38% C -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g23160.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23170.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g23150.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 80.621; most accessible tissue: Minghui63 flag leaf, score: 92.994
vg1213096544 (J) chr12 13096544 GCT G 92.20% 0.00% GCT -> G NA
LOC_Os12g23150.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 83.521; most accessible tissue: Minghui63 flag leaf, score: 93.838
vg1213096561 (J) chr12 13096561 GCGCCGG CGCCGC G 98.60% 0.00% GCGCCGGCGC CGC -> G,TCGCCGGC GCCGC NA
LOC_Os12g23150.1 Alt: G| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os12g23150.1 Alt: TCGCCGGCGCCGC| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 83.032; most accessible tissue: Minghui63 flag leaf, score: 93.756
vg1213096570 (J) chr12 13096570 C G 86.60% 0.00% C -> G NA
LOC_Os12g23150.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.381; most accessible tissue: Minghui63 flag leaf, score: 94.147
vg1213096573 (J) chr12 13096573 G C 67.30% 0.00% C -> G
mr1002 (All); LR P-value: 5.82E-08;
mr1023 (Jap_All); LR P-value: 8.50E-15;
mr1057 (All); LR P-value: 3.53E-06;
mr1142 (Jap_All); LR P-value: 4.15E-14;
mr1178 (Jap_All); LR P-value: 3.26E-10;
mr1182 (All); LR P-value: 5.70E-13;
mr1207 (All); LR P-value: 4.23E-07;
mr1282 (All); LR P-value: 1.58E-10;
mr1401 (Jap_All); LR P-value: 9.10E-07;
mr1489 (Jap_All); LR P-value: 3.80E-14;
mr1563 (Jap_All); LR P-value: 1.01E-08;
mr1584 (Jap_All); LR P-value: 8.54E-07;
mr1606 (All); LR P-value: 1.94E-07;
mr1606 (Jap_All); LR P-value: 9.74E-07;
mr1607 (All); LR P-value: 6.41E-11;
mr1657 (Jap_All); LR P-value: 2.41E-06;
mr1658 (All); LR P-value: 7.46E-09;
mr1730 (All); LR P-value: 1.33E-10;
mr1778 (Jap_All); LR P-value: 2.81E-13;
mr1866 (All); LR P-value: 8.08E-09;
mr1918 (Ind_All); LR P-value: 7.29E-06;
mr1942 (All); LR P-value: 2.69E-10;
mr1993 (All); LR P-value: 8.47E-07;
mr1159_2 (All); LR P-value: 1.80E-07;
mr1189_2 (Jap_All); LR P-value: 1.17E-08;
mr1338_2 (Jap_All); LR P-value: 1.50E-08;
mr1368_2 (Jap_All); LR P-value: 1.29E-10;
mr1607_2 (All); LR P-value: 2.85E-08;
mr1778_2 (Jap_All); LR P-value: 6.97E-14;
mr1815_2 (All); LR P-value: 6.26E-07;
mr1860_2 (Jap_All); LR P-value: 2.42E-06;
mr1910_2 (All); LR P-value: 1.98E-06;
mr1942_2 (All); LR P-value: 2.72E-14
LOC_Os12g23150.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.382; most accessible tissue: Minghui63 flag leaf, score: 94.184