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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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Search Results:

29 variations found. LOC_Os06g41980 (LYK8; putative; expressed), ranging from 25,198,241 bp to 25,200,245 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
vg0625198248 (J) chr06 25198248 ATGC Unkown 72.50% 23.17% ATGC -> A NA
LOC_Os06g41980.1 Alt: A| disruptive_inframe_deletion MODERATE(snpEff)
LOC_Os06g41990.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41990.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 95.081; most accessible tissue: Zhenshan97 young leaf, score: 96.811
vg0625198261 (J) chr06 25198261 T Unkown 90.10% 9.10% T -> C NA
LOC_Os06g41980.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os06g41990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41990.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 95.202; most accessible tissue: Zhenshan97 young leaf, score: 96.922
vg0625198271 (J) chr06 25198271 C Unkown 70.10% 26.94% C -> T NA
LOC_Os06g41980.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os06g41990.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41990.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 95.186; most accessible tissue: Zhenshan97 young leaf, score: 96.964
vg0625198272 (J) chr06 25198272 G C 87.50% 9.90% G -> C NA
LOC_Os06g41980.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g41980.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.212; most accessible tissue: Zhenshan97 young leaf, score: 97.005
vg0625198286 (J) chr06 25198286 G Unkown 98.80% 0.76% G -> C NA
LOC_Os06g41980.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os06g41990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41990.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 95.279; most accessible tissue: Zhenshan97 young leaf, score: 97.045
vg0625198288 (J) chr06 25198288 T C 69.70% 27.25% T -> C NA
LOC_Os06g41980.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g41980.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.301; most accessible tissue: Zhenshan97 young leaf, score: 97.085
vg0625198291 (J) chr06 25198291 C CGCT 79.10% 18.83% C -> CGCT NA
LOC_Os06g41980.1 Alt: CGCT| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os06g41980.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.275; most accessible tissue: Zhenshan97 young leaf, score: 97.085
vg0625198292 (J) chr06 25198292 G Unkown 90.60% 8.48% G -> GCTGT NA
LOC_Os06g41980.1 Alt: GCTGT| frameshift_variant HIGH(snpEff)
LOC_Os06g41990.1 Alt: GCTGT| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41990.2 Alt: GCTGT| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 95.273; most accessible tissue: Zhenshan97 young leaf, score: 97.085
vg0625198293 (J) chr06 25198293 A Unkown 69.60% 27.34% A -> T,C NA
LOC_Os06g41980.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os06g41990.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41990.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41980.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os06g41990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41990.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 95.236; most accessible tissue: Zhenshan97 young leaf, score: 97.045
vg0625198296 (J) chr06 25198296 A G 69.60% 27.34% A -> G NA
LOC_Os06g41980.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g41980.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.286; most accessible tissue: Zhenshan97 young leaf, score: 97.055
vg0625198299 (J) chr06 25198299 G Unkown 69.60% 27.34% G -> A NA
LOC_Os06g41980.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os06g41990.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41990.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 95.272; most accessible tissue: Zhenshan97 young leaf, score: 97.035
vg0625198358 (J) chr06 25198358 C Unkown 96.70% 0.95% C -> A NA
LOC_Os06g41980.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os06g41990.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41990.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 91.938; most accessible tissue: Zhenshan97 young leaf, score: 96.834
vg0625198372 (J) chr06 25198372 A Unkown 99.00% 0.28% A -> C NA
LOC_Os06g41980.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os06g41990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41990.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 91.901; most accessible tissue: Zhenshan97 young leaf, score: 96.944
vg0625198373 (J) chr06 25198373 C Unkown 99.00% 0.28% C -> G NA
LOC_Os06g41980.1 Alt: G| stop_gained HIGH(snpEff)
LOC_Os06g41990.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g41990.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 91.968; most accessible tissue: Zhenshan97 young leaf, score: 96.964
vg0625198384 (J) chr06 25198384 C A 88.80% 0.00% C -> A
mr1104 (All); LMM P-value: 4.48E-06;
mr1107 (All); LMM P-value: 2.33E-06;
mr1226 (All); LMM P-value: 1.33E-07;
mr1408 (All); LR P-value: 1.68E-07;
mr1411 (All); LMM P-value: 2.75E-08;
mr1104_2 (All); LMM P-value: 4.50E-06;
mr1183_2 (Jap_All); LR P-value: 8.72E-07;
mr1226_2 (All); LMM P-value: 7.33E-06;
mr1861_2 (Jap_All); LR P-value: 3.87E-07
LOC_Os06g41980.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.536; most accessible tissue: Zhenshan97 young leaf, score: 96.602
vg0625198577 (J) chr06 25198577 C T 93.50% 0.00% C -> T NA
LOC_Os06g41980.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.429; most accessible tissue: Zhenshan97 flag leaf, score: 96.375
vg0625198745 (J) chr06 25198745 A G 71.00% 0.30% A -> G NA
LOC_Os06g41980.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41980.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 92.574; most accessible tissue: Zhenshan97 flag leaf, score: 96.532
vg0625198979 (J) chr06 25198979 G A 99.50% 0.00% G -> A NA
LOC_Os06g41980.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.922; most accessible tissue: Zhenshan97 young leaf, score: 96.081
vg0625199004 (J) chr06 25199004 T TCTCCGG 99.60% 0.00% T -> TCTCCGG NA
LOC_Os06g41980.1 Alt: TCTCCGG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 91.770; most accessible tissue: Zhenshan97 young leaf, score: 96.015
vg0625199096 (J) chr06 25199096 C T 86.00% 0.00% C -> T NA
LOC_Os06g41980.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.378; most accessible tissue: Zhenshan97 young leaf, score: 95.930
vg0625199353 (J) chr06 25199353 C T 91.00% 0.00% T -> C NA
LOC_Os06g41980.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.463; most accessible tissue: Zhenshan97 young leaf, score: 97.278
vg0625199428 (J) chr06 25199428 C T 83.70% 0.00% C -> T NA
LOC_Os06g41980.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 92.278; most accessible tissue: Zhenshan97 young leaf, score: 97.459
vg0625199534 (J) chr06 25199534 C T 87.50% 0.28% C -> T NA
LOC_Os06g41980.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41980.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 93.143; most accessible tissue: Zhenshan97 young leaf, score: 97.670
vg0625199781 (J) chr06 25199781 A G 71.10% 0.25% A -> G NA
LOC_Os06g41980.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g41980.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.544; most accessible tissue: Zhenshan97 young leaf, score: 98.430
vg0625199786 (J) chr06 25199786 C T 87.50% 0.25% C -> T NA
LOC_Os06g41980.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41980.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.500; most accessible tissue: Zhenshan97 young leaf, score: 98.422
vg0625199926 (J) chr06 25199926 G T 99.80% 0.00% G -> T NA
LOC_Os06g41980.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 96.430; most accessible tissue: Zhenshan97 young leaf, score: 98.778
vg0625200027 (J) chr06 25200027 G A 87.80% 0.00% G -> A
mr1226 (All); LMM P-value: 1.16E-06;
mr1408 (All); LR P-value: 2.93E-07;
mr1411 (All); LMM P-value: 1.66E-07;
mr1861_2 (Jap_All); LR P-value: 2.04E-06
LOC_Os06g41980.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 96.990; most accessible tissue: Zhenshan97 young leaf, score: 98.978
vg0625200123 (J) chr06 25200123 C G 99.50% 0.00% C -> G NA
LOC_Os06g41980.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 94.895; most accessible tissue: Zhenshan97 young leaf, score: 98.719
STR0625199780 (J) chr06 25199780 CACCGTC CGCCGTT 78.70% 0.00% CACCGTC -> CGCCGTT,CG CCGTC NA