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Search Results:

14 variations found. LOC_Os12g40120 (B3 DNA binding domain containing protein; expressed), ranging from 24,818,050 bp to 24,820,047 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
vg1224818100 (J) chr12 24818100 A G 99.80% 0.00% A -> G NA
LOC_Os12g40120.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os12g40130.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g40115.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 69.430; most accessible tissue: Zhenshan97 panicle, score: 82.336
vg1224818466 (J) chr12 24818466 A T 89.90% 0.15% A -> T
mr1730 (All); LR P-value: 3.40E-10;
mr1193_2 (All); LR P-value: 2.29E-10;
mr1344_2 (All); LR P-value: 2.54E-06;
mr1347_2 (All); LR P-value: 5.26E-08;
mr1587_2 (All); LR P-value: 1.45E-16;
mr1829_2 (All); LR P-value: 1.35E-08
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g40130.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40115.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40120.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 54.873; most accessible tissue: Callus, score: 89.080
vg1224818756 (J) chr12 24818756 T C 99.70% 0.00% T -> C NA
LOC_Os12g40120.1 Alt: C| splice_acceptor_variant&intron_variant HIGH(snpEff)
LOC_Os12g40130.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g40140.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 50.403; most accessible tissue: Callus, score: 88.891
vg1224818794 (J) chr12 24818794 A G 89.70% 0.15% A -> G
mr1126 (All); LR P-value: 2.43E-06;
mr1158 (All); LR P-value: 1.28E-15;
mr1730 (All); LR P-value: 9.94E-10;
mr1193_2 (All); LR P-value: 1.51E-10;
mr1344_2 (All); LR P-value: 5.28E-06;
mr1587_2 (All); LR P-value: 4.23E-17;
mr1829_2 (All); LR P-value: 1.16E-08
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g40130.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40140.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40115.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40120.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 49.327; most accessible tissue: Callus, score: 88.891
vg1224818875 (J) chr12 24818875 A G 89.90% 0.15% A -> G
mr1730 (All); LR P-value: 3.40E-10;
mr1193_2 (All); LR P-value: 2.29E-10;
mr1344_2 (All); LR P-value: 2.54E-06;
mr1347_2 (All); LR P-value: 5.26E-08;
mr1587_2 (All); LR P-value: 1.45E-16;
mr1829_2 (All); LR P-value: 1.35E-08
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g40130.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40140.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40115.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40120.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 48.157; most accessible tissue: Zhenshan97 young leaf, score: 70.177
vg1224818910 (J) chr12 24818910 T C 67.00% 0.00% C -> T
Grain_width (Jap_All); LR P-value: 3.69E-13;
mr1013 (All); LR P-value: 1.85E-13;
mr1271 (Jap_All); LR P-value: 7.13E-08;
mr1364 (Jap_All); LR P-value: 7.38E-06;
mr1403 (All); LR P-value: 5.17E-09;
mr1415 (All); LR P-value: 1.98E-06;
mr1422 (All); LR P-value: 9.09E-19;
mr1443 (Jap_All); LR P-value: 2.14E-06;
mr1539 (All); LR P-value: 3.68E-09;
mr1540 (All); LR P-value: 7.57E-16;
mr1567 (All); LR P-value: 1.98E-06;
mr1732 (All); LR P-value: 7.28E-16;
mr1864 (Jap_All); LR P-value: 1.83E-08;
mr1896 (Jap_All); LR P-value: 7.57E-06;
mr1942 (Jap_All); LR P-value: 6.15E-06;
mr1089_2 (Jap_All); LR P-value: 1.29E-09;
mr1090_2 (Jap_All); LR P-value: 1.36E-07;
mr1096_2 (Jap_All); LR P-value: 2.12E-06;
mr1097_2 (Jap_All); LR P-value: 6.03E-08;
mr1121_2 (Jap_All); LR P-value: 1.48E-06;
mr1211_2 (Jap_All); LR P-value: 3.30E-06;
mr1248_2 (Jap_All); LR P-value: 1.45E-06;
mr1295_2 (Jap_All); LR P-value: 1.66E-06;
mr1347_2 (All); LR P-value: 3.14E-09;
mr1539_2 (Jap_All); LR P-value: 1.47E-15;
mr1540_2 (Jap_All); LR P-value: 2.41E-15;
mr1567_2 (All); LR P-value: 1.06E-06;
mr1580_2 (Jap_All); LR P-value: 3.21E-10;
mr1671_2 (Jap_All); LR P-value: 1.10E-07;
mr1732_2 (Jap_All); LR P-value: 7.38E-14;
mr1771_2 (Jap_All); LR P-value: 7.89E-10;
mr1789_2 (Jap_All); LR P-value: 3.42E-11;
mr1805_2 (Jap_All); LR P-value: 1.41E-08;
mr1825_2 (Jap_All); LR P-value: 4.74E-10;
mr1862_2 (Jap_All); LR P-value: 1.91E-08
LOC_Os12g40120.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 47.305; most accessible tissue: Zhenshan97 young leaf, score: 65.804
vg1224818915 (J) chr12 24818915 C T 93.30% 0.00% C -> T NA
LOC_Os12g40120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 47.348; most accessible tissue: Zhenshan97 young leaf, score: 66.320
vg1224819153 (J) chr12 24819153 G A 99.90% 0.00% G -> A NA
LOC_Os12g40120.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 50.335; most accessible tissue: Zhenshan97 panicle, score: 73.605
vg1224819316 (J) chr12 24819316 T C 89.90% 0.15% T -> C
mr1158 (All); LR P-value: 5.98E-15;
mr1730 (All); LR P-value: 3.21E-10;
mr1344_2 (All); LR P-value: 3.80E-06;
mr1587_2 (All); LR P-value: 3.64E-16
LOC_Os12g40120.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g40120.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 50.201; most accessible tissue: Zhenshan97 panicle, score: 74.671
vg1224819418 (J) chr12 24819418 GAA G 93.80% 0.00% GAA -> G NA
LOC_Os12g40130.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40140.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40115.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40120.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 52.171; most accessible tissue: Zhenshan97 panicle, score: 76.605
vg1224819564 (J) chr12 24819564 G A 77.40% 0.00% A -> G
Grain_width (Jap_All); LR P-value: 3.69E-13;
mr1077 (All); LR P-value: 1.48E-18;
mr1271 (Jap_All); LR P-value: 7.13E-08;
mr1300 (All); LR P-value: 3.48E-22;
mr1364 (All); LR P-value: 4.58E-08;
mr1364 (Jap_All); LR P-value: 7.38E-06;
mr1443 (All); LR P-value: 2.83E-07;
mr1443 (Jap_All); LR P-value: 2.14E-06;
mr1563 (All); LR P-value: 2.48E-46;
mr1741 (All); LR P-value: 4.59E-12;
mr1864 (Jap_All); LR P-value: 1.83E-08;
mr1896 (Jap_All); LR P-value: 7.57E-06;
mr1942 (Jap_All); LR P-value: 6.15E-06;
mr1045_2 (All); LR P-value: 3.49E-07;
mr1077_2 (All); LR P-value: 2.71E-25;
mr1089_2 (Jap_All); LR P-value: 1.29E-09;
mr1090_2 (Jap_All); LR P-value: 1.36E-07;
mr1096_2 (Jap_All); LR P-value: 2.12E-06;
mr1097_2 (Jap_All); LR P-value: 6.03E-08;
mr1121_2 (Jap_All); LR P-value: 1.48E-06;
mr1211_2 (Jap_All); LR P-value: 3.30E-06;
mr1248_2 (Jap_All); LR P-value: 1.45E-06;
mr1252_2 (All); LR P-value: 4.04E-07;
mr1295_2 (Jap_All); LR P-value: 1.66E-06;
mr1539_2 (All); LR P-value: 2.65E-18;
mr1539_2 (Jap_All); LR P-value: 1.47E-15;
mr1540_2 (Jap_All); LR P-value: 2.41E-15;
mr1580_2 (Jap_All); LR P-value: 3.21E-10;
mr1671_2 (Jap_All); LR P-value: 1.10E-07;
mr1679_2 (All); LR P-value: 9.61E-24;
mr1732_2 (Jap_All); LR P-value: 7.38E-14;
mr1741_2 (All); LR P-value: 2.92E-09;
mr1768_2 (All); LR P-value: 4.58E-27;
mr1771_2 (All); LR P-value: 2.39E-44;
mr1771_2 (Jap_All); LR P-value: 7.89E-10;
mr1784_2 (All); LR P-value: 3.37E-44;
mr1785_2 (All); LR P-value: 1.05E-06;
mr1789_2 (All); LR P-value: 1.10E-29;
mr1789_2 (Jap_All); LR P-value: 3.42E-11;
mr1805_2 (Jap_All); LR P-value: 1.41E-08;
mr1825_2 (Jap_All); LR P-value: 4.74E-10;
mr1827_2 (All); LR P-value: 6.51E-14;
mr1842_2 (All); LR P-value: 2.39E-16;
mr1844_2 (All); LR P-value: 9.79E-11;
mr1862_2 (All); LR P-value: 4.44E-41;
mr1862_2 (Jap_All); LR P-value: 1.91E-08;
mr1902_2 (All); LR P-value: 1.07E-15
LOC_Os12g40130.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40140.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40115.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40120.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 49.537; most accessible tissue: Callus, score: 76.668
vg1224819675 (J) chr12 24819675 C T 89.80% 0.11% C -> T
mr1126 (All); LR P-value: 3.29E-06;
mr1730 (All); LR P-value: 8.66E-10;
mr1344_2 (All); LR P-value: 5.21E-06;
mr1587_2 (All); LR P-value: 2.84E-16;
mr1829_2 (All); LR P-value: 9.45E-09
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g40130.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40115.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40120.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 53.901; most accessible tissue: Zhenshan97 young leaf, score: 78.347
vg1224819735 (J) chr12 24819735 T G 89.90% 0.13% T -> G
mr1730 (All); LR P-value: 3.40E-10;
mr1193_2 (All); LR P-value: 2.29E-10;
mr1344_2 (All); LR P-value: 2.54E-06;
mr1347_2 (All); LR P-value: 5.26E-08;
mr1587_2 (All); LR P-value: 1.45E-16;
mr1829_2 (All); LR P-value: 1.35E-08
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g40130.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40140.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40115.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40120.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 53.582; most accessible tissue: Zhenshan97 young leaf, score: 77.736
STR1224818902 (J) chr12 24818902 GTCTTGG TTTTGCT GTCTTGG TCTTGCC 66.10% 0.00% GTCTTGGTCT TGCC -> GTCTTGGTTT TGCT NA