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Search Results:

22 variations found. LOC_Os08g39550 (polygalacturonase inhibitor 2 precursor; putative; expressed), ranging from 25,015,690 bp to 25,017,363 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
vg0825015742 (J) chr08 25015742 CTAT C 99.60% 0.00% CTAT -> C NA
LOC_Os08g39550.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g39540.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 42.300; most accessible tissue: Callus, score: 74.133
vg0825015850 (J) chr08 25015850 A G 89.50% 0.11% A -> G
mr1874 (All); LMM P-value: 1.99E-15; LR P-value: 1.97E-22;
mr1874 (Ind_All); LMM P-value: 2.32E-15; LR P-value: 1.81E-20;
mr1709_2 (All); LR P-value: 7.40E-10;
mr1874_2 (All); LMM P-value: 1.78E-17; LR P-value: 1.51E-23;
mr1874_2 (Ind_All); LMM P-value: 9.56E-17; LR P-value: 3.78E-21
LOC_Os08g39550.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39540.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 65.592; most accessible tissue: Zhenshan97 flower, score: 78.853
vg0825015887 (J) chr08 25015887 C CA 99.50% 0.00% C -> CA NA
LOC_Os08g39550.1 Alt: CA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39540.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 68.689; most accessible tissue: Zhenshan97 panicle, score: 83.904
vg0825015902 (J) chr08 25015902 A G 80.40% 0.00% G -> A,T
Grain_length (Jap_All); LR P-value: 2.92E-15;
mr1026 (Jap_All); LR P-value: 1.67E-06;
mr1229 (Jap_All); LR P-value: 3.99E-07;
mr1401 (Jap_All); LR P-value: 1.96E-06;
mr1606 (Jap_All); LR P-value: 5.31E-06;
mr1826 (All); LR P-value: 6.26E-07;
mr1977 (All); LR P-value: 3.01E-08;
mr1977 (Jap_All); LR P-value: 9.07E-06;
mr1063_2 (Jap_All); LR P-value: 9.71E-06;
mr1077_2 (Jap_All); LR P-value: 4.53E-07;
mr1229_2 (All); LR P-value: 2.47E-07;
mr1229_2 (Jap_All); LR P-value: 8.55E-07;
mr1486_2 (Jap_All); LR P-value: 1.61E-09;
mr1502_2 (Jap_All); LR P-value: 1.21E-07;
mr1570_2 (Jap_All); LR P-value: 8.68E-07;
mr1763_2 (All); LR P-value: 1.96E-06;
mr1789_2 (All); LR P-value: 2.03E-28;
mr1789_2 (Jap_All); LR P-value: 6.57E-11;
mr1871_2 (Jap_All); LR P-value: 1.49E-08;
mr1880_2 (All); LR P-value: 1.02E-07;
mr1880_2 (Jap_All); LR P-value: 2.16E-07
LOC_Os08g39550.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39550.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 70.249; most accessible tissue: Zhenshan97 panicle, score: 87.764
vg0825015968 (J) chr08 25015968 TCACA TCA 69.30% 0.42% TCACA -> TCA,T NA
LOC_Os08g39550.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
LOC_Os08g39550.1 Alt: TCA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39540.1 Alt: TCA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.458; most accessible tissue: Zhenshan97 panicle, score: 95.548
vg0825015970 (J) chr08 25015970 A T 71.30% 20.88% A -> T NA
LOC_Os08g39550.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 88.500; most accessible tissue: Zhenshan97 panicle, score: 95.602
vg0825015972 (J) chr08 25015972 A T 89.30% 0.34% A -> T NA
LOC_Os08g39550.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 88.477; most accessible tissue: Zhenshan97 panicle, score: 95.602
vg0825016021 (J) chr08 25016021 G A 99.80% 0.00% G -> A NA
LOC_Os08g39550.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g39540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 91.618; most accessible tissue: Zhenshan97 panicle, score: 96.801
vg0825016142 (J) chr08 25016142 T G 95.30% 0.00% T -> G NA
LOC_Os08g39550.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39540.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.168; most accessible tissue: Zhenshan97 panicle, score: 97.577
vg0825016470 (J) chr08 25016470 C A 69.30% 0.36% C -> A
mr1874 (All); LMM P-value: 8.52E-18; LR P-value: 2.13E-40;
mr1874 (Ind_All); LMM P-value: 4.30E-16; LR P-value: 6.42E-22;
mr1004_2 (All); LR P-value: 7.93E-08;
mr1193_2 (All); LR P-value: 8.41E-11;
mr1699_2 (All); LMM P-value: 6.10E-08;
mr1699_2 (Ind_All); LMM P-value: 3.16E-07; LR P-value: 1.57E-11;
mr1874_2 (All); LMM P-value: 3.75E-21; LR P-value: 3.05E-58;
mr1874_2 (Ind_All); LMM P-value: 2.78E-20; LR P-value: 4.90E-30
LOC_Os08g39550.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g39550.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 89.412; most accessible tissue: Zhenshan97 panicle, score: 95.806
vg0825016494 (J) chr08 25016494 G T 89.50% 0.28% G -> T
mr1874 (All); LMM P-value: 1.99E-15; LR P-value: 1.97E-22;
mr1874 (Ind_All); LMM P-value: 2.32E-15; LR P-value: 1.81E-20;
mr1709_2 (All); LR P-value: 7.40E-10;
mr1874_2 (All); LMM P-value: 1.78E-17; LR P-value: 1.51E-23;
mr1874_2 (Ind_All); LMM P-value: 9.56E-17; LR P-value: 3.78E-21
LOC_Os08g39550.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g39550.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 89.477; most accessible tissue: Minghui63 panicle, score: 95.701
vg0825016500 (J) chr08 25016500 G A 99.90% 0.00% G -> A NA
LOC_Os08g39550.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.420; most accessible tissue: Minghui63 panicle, score: 95.468
vg0825016648 (J) chr08 25016648 C T 99.80% 0.00% C -> T NA
LOC_Os08g39550.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os08g39540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 85.615; most accessible tissue: Zhenshan97 panicle, score: 94.112
vg0825016692 (J) chr08 25016692 G A 99.80% 0.00% G -> A NA
LOC_Os08g39550.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.204; most accessible tissue: Minghui63 panicle, score: 94.127
vg0825016854 (J) chr08 25016854 G A 89.50% 0.23% G -> A
mr1874 (All); LMM P-value: 9.54E-15; LR P-value: 4.84E-22;
mr1874 (Ind_All); LMM P-value: 8.76E-15; LR P-value: 5.54E-20;
mr1709_2 (All); LR P-value: 2.04E-09;
mr1874_2 (All); LMM P-value: 3.08E-18; LR P-value: 1.56E-24;
mr1874_2 (Ind_All); LMM P-value: 2.01E-17; LR P-value: 3.99E-22
LOC_Os08g39550.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g39550.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.260; most accessible tissue: Minghui63 panicle, score: 94.218
vg0825016896 (J) chr08 25016896 G A 69.30% 0.11% G -> A
mr1874 (All); LMM P-value: 3.78E-18; LR P-value: 7.37E-41;
mr1874 (Ind_All); LMM P-value: 2.10E-16; LR P-value: 2.13E-22;
mr1004_2 (All); LR P-value: 3.29E-08;
mr1193_2 (All); LR P-value: 1.64E-10;
mr1699_2 (All); LMM P-value: 6.71E-08;
mr1699_2 (Ind_All); LMM P-value: 3.89E-07; LR P-value: 1.34E-11;
mr1874_2 (All); LMM P-value: 1.21E-21; LR P-value: 9.52E-59;
mr1874_2 (Ind_All); LMM P-value: 7.17E-21; LR P-value: 1.67E-30
LOC_Os08g39550.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g39550.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.203; most accessible tissue: Zhenshan97 panicle, score: 94.112
vg0825017058 (J) chr08 25017058 G C 94.50% 0.00% G -> C NA
LOC_Os08g39550.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 90.774; most accessible tissue: Zhenshan97 panicle, score: 96.894
vg0825017059 (J) chr08 25017059 C T 94.50% 0.00% C -> T NA
LOC_Os08g39550.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 90.793; most accessible tissue: Zhenshan97 panicle, score: 96.924
vg0825017097 (J) chr08 25017097 A G 69.10% 0.00% A -> G
mr1874 (All); LMM P-value: 1.73E-18; LR P-value: 1.32E-41;
mr1874 (Ind_All); LMM P-value: 2.60E-16; LR P-value: 2.81E-22;
mr1004_2 (All); LR P-value: 4.80E-08;
mr1193_2 (All); LR P-value: 1.92E-11;
mr1587_2 (All); LR P-value: 1.38E-15;
mr1699_2 (All); LMM P-value: 6.61E-08;
mr1699_2 (Ind_All); LMM P-value: 3.32E-07; LR P-value: 1.28E-11;
mr1874_2 (All); LMM P-value: 1.97E-22; LR P-value: 2.98E-60;
mr1874_2 (Ind_All); LMM P-value: 5.76E-21; LR P-value: 8.39E-31
LOC_Os08g39550.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.392; most accessible tissue: Zhenshan97 panicle, score: 96.982
vg0825017138 (J) chr08 25017138 C T 93.90% 0.00% C -> T NA
LOC_Os08g39550.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.188; most accessible tissue: Zhenshan97 panicle, score: 97.512
vg0825017270 (J) chr08 25017270 CGAG C 89.90% 0.00% CGAG -> C NA
LOC_Os08g39550.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 96.233; most accessible tissue: Zhenshan97 panicle, score: 98.676
STR0825015969 (J) chr08 25015969 CACACAC CAC 73.90% 0.00% CACACAC -> CAC,CACAC NA