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Search Results:

38 variations found. LOC_Os10g23830 (PPR repeat domain containing protein; putative; expressed), ranging from 12,223,906 bp to 12,224,380 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
vg1012223906 (J) chr10 12223906 A G 49.80% 49.28% A -> G NA
LOC_Os10g23830.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g23840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g23820-LOC_Os10g23830 Alt: G| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 8.866; most accessible tissue: Callus, score: 26.513
vg1012223908 (J) chr10 12223908 T C 30.60% 50.00% T -> C NA
LOC_Os10g23830.1 Alt: C| start_lost HIGH(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.866; most accessible tissue: Callus, score: 26.513
vg1012223911 (J) chr10 12223911 C T 30.70% 50.02% C -> T NA
LOC_Os10g23830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.866; most accessible tissue: Callus, score: 26.513
vg1012223914 (J) chr10 12223914 G A 49.70% 49.30% G -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.866; most accessible tissue: Callus, score: 26.513
vg1012223917 (J) chr10 12223917 T G 49.70% 49.30% T -> G NA
LOC_Os10g23830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.866; most accessible tissue: Callus, score: 26.513
vg1012223918 (J) chr10 12223918 G A 50.00% 49.22% G -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.866; most accessible tissue: Callus, score: 26.513
vg1012223929 (J) chr10 12223929 C T 50.00% 49.41% C -> T NA
LOC_Os10g23830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.042; most accessible tissue: Callus, score: 51.074
vg1012223933 (J) chr10 12223933 G A 49.60% 49.34% G -> A NA
LOC_Os10g23830.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.099; most accessible tissue: Callus, score: 51.074
vg1012223948 (J) chr10 12223948 C T 49.80% 49.34% C -> T NA
LOC_Os10g23830.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.598; most accessible tissue: Callus, score: 51.074
vg1012223963 (J) chr10 12223963 T C 30.90% 50.97% T -> C NA
LOC_Os10g23830.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.598; most accessible tissue: Callus, score: 51.074
vg1012223964 (J) chr10 12223964 G A 49.90% 49.34% G -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.598; most accessible tissue: Callus, score: 51.074
vg1012223969 (J) chr10 12223969 G C 31.60% 50.53% G -> C NA
LOC_Os10g23830.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.655; most accessible tissue: Callus, score: 51.074
vg1012223994 (J) chr10 12223994 A G 49.00% 49.49% A -> G NA
LOC_Os10g23830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.537; most accessible tissue: Callus, score: 51.074
vg1012224002 (J) chr10 12224002 T C 49.00% 49.62% T -> C NA
LOC_Os10g23830.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.424; most accessible tissue: Callus, score: 51.074
vg1012224010 (J) chr10 12224010 G A 50.40% 49.24% G -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.424; most accessible tissue: Callus, score: 51.074
vg1012224030 (J) chr10 12224030 C T 50.30% 49.24% C -> T NA
LOC_Os10g23830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.887; most accessible tissue: Callus, score: 51.074
vg1012224034 (J) chr10 12224034 A G 31.30% 49.98% A -> G NA
LOC_Os10g23830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.887; most accessible tissue: Callus, score: 51.074
vg1012224036 (J) chr10 12224036 A G 48.60% 49.70% A -> G NA
LOC_Os10g23830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.887; most accessible tissue: Callus, score: 51.074
vg1012224052 (J) chr10 12224052 G A 48.80% 49.79% G -> A NA
LOC_Os10g23830.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.774; most accessible tissue: Callus, score: 51.074
vg1012224057 (J) chr10 12224057 G A 31.30% 49.87% G -> A
mr1157 (Ind_All); LR P-value: 5.05E-06;
mr1328 (Ind_All); LR P-value: 9.21E-08;
mr1415 (All); LR P-value: 1.93E-06;
mr1420 (All); LR P-value: 1.42E-06;
mr1446 (Ind_All); LR P-value: 6.62E-08;
mr1567 (All); LR P-value: 1.93E-06;
mr1689 (Ind_All); LR P-value: 8.42E-06;
mr1909 (All); LR P-value: 3.30E-14;
mr1921 (All); LR P-value: 1.96E-11;
mr1158_2 (All); LR P-value: 8.26E-08;
mr1369_2 (All); LR P-value: 4.98E-07;
mr1446_2 (Ind_All); LMM P-value: 4.33E-06; LR P-value: 2.08E-09;
mr1453_2 (All); LR P-value: 1.12E-07;
mr1467_2 (All); LR P-value: 1.75E-06;
mr1556_2 (All); LR P-value: 4.59E-06;
mr1567_2 (All); LR P-value: 1.96E-09;
mr1567_2 (Ind_All); LR P-value: 6.39E-06;
mr1633_2 (All); LR P-value: 7.10E-06;
mr1641_2 (All); LR P-value: 5.75E-12;
mr1706_2 (All); LR P-value: 2.79E-07;
mr1764_2 (All); LR P-value: 6.27E-06;
mr1811_2 (All); LR P-value: 3.77E-06;
mr1921_2 (All); LR P-value: 1.34E-08;
mr1951_2 (All); LR P-value: 4.94E-06
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.887; most accessible tissue: Callus, score: 51.074
vg1012224060 (J) chr10 12224060 C T 50.30% 48.92% C -> T NA
LOC_Os10g23830.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.774; most accessible tissue: Callus, score: 51.074
vg1012224061 (J) chr10 12224061 G A 49.20% 49.66% G -> A,T NA
LOC_Os10g23830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.774; most accessible tissue: Callus, score: 51.074
vg1012224073 (J) chr10 12224073 G A 48.60% 49.79% G -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.253; most accessible tissue: Callus, score: 51.074
vg1012224079 (J) chr10 12224079 T C 48.30% 50.02% T -> C NA
LOC_Os10g23830.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.993; most accessible tissue: Callus, score: 37.216
vg1012224094 (J) chr10 12224094 G A 49.20% 49.64% G -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.993; most accessible tissue: Callus, score: 37.216
vg1012224107 (J) chr10 12224107 C G 31.20% 50.17% C -> G
mr1157 (All); LR P-value: 1.32E-07;
mr1157 (Ind_All); LR P-value: 3.47E-06;
mr1328 (All); LR P-value: 1.11E-09;
mr1328 (Ind_All); LR P-value: 3.17E-08;
mr1446 (All); LR P-value: 3.84E-10;
mr1446 (Ind_All); LMM P-value: 7.90E-06; LR P-value: 5.62E-08;
mr1446_2 (All); LMM P-value: 4.90E-07; LR P-value: 1.04E-13;
mr1446_2 (Ind_All); LMM P-value: 6.59E-06; LR P-value: 2.20E-09;
mr1567_2 (Ind_All); LR P-value: 3.97E-06
LOC_Os10g23830.1 Alt: G| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.993; most accessible tissue: Callus, score: 37.216
vg1012224109 (J) chr10 12224109 T C 48.30% 49.85% T -> C NA
LOC_Os10g23830.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.993; most accessible tissue: Callus, score: 37.216
vg1012224142 (J) chr10 12224142 G A 49.10% 49.01% G -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.993; most accessible tissue: Callus, score: 37.216
vg1012224147 (J) chr10 12224147 G A 48.70% 49.53% G -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.993; most accessible tissue: Callus, score: 37.216
vg1012224168 (J) chr10 12224168 G A 49.00% 48.94% G -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.935; most accessible tissue: Callus, score: 37.216
vg1012224171 (J) chr10 12224171 A G 48.70% 49.28% A -> G NA
LOC_Os10g23830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.876; most accessible tissue: Callus, score: 37.216
vg1012224194 (J) chr10 12224194 G A 31.10% 49.89% G -> A
mr1157 (All); LR P-value: 1.01E-07;
mr1157 (Ind_All); LR P-value: 1.58E-06;
mr1328 (All); LR P-value: 1.60E-09;
mr1328 (Ind_All); LMM P-value: 7.00E-06; LR P-value: 2.25E-08;
mr1446 (All); LR P-value: 2.84E-10;
mr1446 (Ind_All); LMM P-value: 3.23E-06; LR P-value: 2.25E-08;
mr1236_2 (All); LR P-value: 8.08E-06;
mr1419_2 (All); LR P-value: 9.86E-06;
mr1446_2 (All); LMM P-value: 3.07E-07; LR P-value: 9.38E-14;
mr1446_2 (Ind_All); LMM P-value: 1.84E-06; LR P-value: 8.21E-10;
mr1567_2 (Ind_All); LR P-value: 3.75E-06
LOC_Os10g23830.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.255; most accessible tissue: Callus, score: 56.934
vg1012224195 (J) chr10 12224195 C A 49.10% 48.96% C -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.255; most accessible tissue: Callus, score: 56.934
vg1012224216 (J) chr10 12224216 G A 49.30% 48.56% G -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.255; most accessible tissue: Callus, score: 56.934
vg1012224239 (J) chr10 12224239 T C 48.60% 49.60% T -> C
mr1157 (Ind_All); LR P-value: 8.45E-06;
mr1328 (Ind_All); LR P-value: 1.60E-07;
mr1446 (Ind_All); LR P-value: 1.89E-07;
mr1654 (All); LR P-value: 3.07E-06;
mr1815 (All); LR P-value: 2.86E-06;
mr1446_2 (Ind_All); LMM P-value: 8.06E-06; LR P-value: 1.15E-08
LOC_Os10g23830.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.138; most accessible tissue: Callus, score: 56.934
vg1012224276 (J) chr10 12224276 G A 49.30% 49.32% G -> A NA
LOC_Os10g23830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.017; most accessible tissue: Callus, score: 56.934
vg1012224308 (J) chr10 12224308 C T 50.00% 49.03% C -> T NA
LOC_Os10g23830.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.196; most accessible tissue: Callus, score: 56.934
vg1012224371 (J) chr10 12224371 C G 31.40% 49.83% C -> G
mr1157 (All); LR P-value: 1.79E-07;
mr1157 (Ind_All); LR P-value: 4.99E-06;
mr1328 (All); LR P-value: 2.31E-09;
mr1328 (Ind_All); LR P-value: 6.91E-08;
mr1446 (All); LR P-value: 9.15E-10;
mr1446 (Ind_All); LR P-value: 1.45E-07;
mr1446_2 (All); LMM P-value: 1.26E-06; LR P-value: 2.34E-13;
mr1446_2 (Ind_All); LR P-value: 4.50E-09;
mr1567_2 (Ind_All); LR P-value: 7.60E-06
LOC_Os10g23830.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g23830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 27.003; most accessible tissue: Zhenshan97 panicle, score: 49.416