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Search Results:

5 variations found. LOC_Os07g05150 (Skp1 family; dimerisation domain containing protein; expressed), ranging from 2,285,847 bp to 2,286,321 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
vg0702285881 (J) chr07 2285881 T TTCC 98.00% 0.00% T -> TTCC NA
LOC_Os07g05150.1 Alt: TTCC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 49.588; most accessible tissue: Zhenshan97 panicle, score: 86.058
vg0702285896 (J) chr07 2285896 T C 57.70% 0.00% C -> T
mr1004 (All); LR P-value: 3.12E-06;
mr1005 (All); LR P-value: 4.00E-11;
mr1059 (All); LR P-value: 1.01E-14;
mr1675 (All); LR P-value: 7.29E-15;
mr1874 (All); LR P-value: 3.49E-15;
mr1950 (All); LR P-value: 1.60E-15;
mr1995 (All); LR P-value: 3.10E-16;
mr1158_2 (Ind_All); LR P-value: 1.58E-10;
mr1383_2 (Ind_All); LR P-value: 1.62E-11;
mr1520_2 (All); LR P-value: 1.55E-11;
mr1645_2 (All); LR P-value: 5.74E-08;
mr1654_2 (All); LR P-value: 6.13E-08;
mr1874_2 (All); LR P-value: 1.70E-19
LOC_Os07g05150.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 48.346; most accessible tissue: Zhenshan97 panicle, score: 84.374
vg0702286198 (J) chr07 2286198 C T 57.60% 0.00% T -> C
mr1004 (All); LR P-value: 7.07E-07;
mr1005 (All); LR P-value: 5.82E-12;
mr1874 (All); LR P-value: 1.72E-13;
mr1950 (All); LR P-value: 1.12E-15;
mr1158_2 (Ind_All); LR P-value: 2.40E-09;
mr1383_2 (Ind_All); LR P-value: 2.79E-11;
mr1654_2 (All); LR P-value: 1.87E-07;
mr1874_2 (All); LR P-value: 1.47E-18
LOC_Os07g05150.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 44.795; most accessible tissue: Callus, score: 59.322
vg0702286225 (J) chr07 2286225 A G 92.90% 0.00% A -> G NA
LOC_Os07g05150.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 47.891; most accessible tissue: Callus, score: 59.322
STR0702285882 (J) chr07 2285882 TCCTCCT CCTC TCCTCCT CCTCCTC 97.80% 0.00% TCCTCCTCCT C -> TCCTCCTCCT CCTC NA