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Search Results:

24 variations found. LOC_Os04g41140 (PPR repeat containing protein; expressed), ranging from 24,399,161 bp to 24,402,461 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
vg0424399275 (J) chr04 24399275 T G 75.20% 0.00% T -> G NA
LOC_Os04g41130.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41150.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41140.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 48.591; most accessible tissue: Callus, score: 77.397
vg0424399282 (J) chr04 24399282 A T 94.20% 0.00% A -> T NA
LOC_Os04g41130.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41150.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41140.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 48.791; most accessible tissue: Callus, score: 77.397
vg0424399292 (J) chr04 24399292 C T 75.40% 0.00% C -> T NA
LOC_Os04g41130.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41150.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41140.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 48.550; most accessible tissue: Callus, score: 77.397
vg0424400607 (J) chr04 24400607 G A 96.00% 0.00% G -> A NA
LOC_Os04g41140.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 51.227; most accessible tissue: Zhenshan97 young leaf, score: 84.431
vg0424400640 (J) chr04 24400640 T C 94.20% 0.00% T -> C NA
LOC_Os04g41140.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 49.523; most accessible tissue: Zhenshan97 young leaf, score: 80.848
vg0424400921 (J) chr04 24400921 A C 75.30% 0.00% A -> C NA
LOC_Os04g41140.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 58.575; most accessible tissue: Zhenshan97 young leaf, score: 77.736
vg0424400923 (J) chr04 24400923 C A 75.30% 0.00% C -> A NA
LOC_Os04g41140.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 58.683; most accessible tissue: Zhenshan97 young leaf, score: 77.736
vg0424401445 (J) chr04 24401445 A G 75.00% 0.00% A -> G,C NA
LOC_Os04g41140.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os04g41150.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g41140.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 65.290; most accessible tissue: Zhenshan97 young leaf, score: 88.637
vg0424401893 (J) chr04 24401893 C A 82.60% 0.00% C -> A
mr1707_2 (All); LR P-value: 1.21E-08;
mr1860_2 (All); LR P-value: 2.40E-09;
mr1860_2 (Ind_All); LR P-value: 8.19E-06
LOC_Os04g41140.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 88.319; most accessible tissue: Zhenshan97 young leaf, score: 94.981
vg0424401969 (J) chr04 24401969 T C 98.60% 0.00% T -> C NA
LOC_Os04g41140.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.125; most accessible tissue: Minghui63 flower, score: 95.456
vg0424402264 (J) chr04 24402264 GGCCGCG GC TGCCGCG GC 94.20% 0.00% GGCCGCGGC -> TGCCGCGGC, G NA
LOC_Os04g41140.1 Alt: G| frameshift_variant HIGH(snpEff)
LOC_Os04g41140.1 Alt: TGCCGCGGC| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 94.828; most accessible tissue: Minghui63 panicle, score: 97.857
vg0424402267 (J) chr04 24402267 C CGCG 99.40% 0.00% C -> CGCG NA
LOC_Os04g41140.1 Alt: CGCG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 94.845; most accessible tissue: Minghui63 panicle, score: 97.877
vg0424402275 (J) chr04 24402275 C T 93.90% 0.30% C -> T NA
LOC_Os04g41140.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41140.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 94.888; most accessible tissue: Minghui63 panicle, score: 97.915
vg0424402284 (J) chr04 24402284 G A 99.40% 0.47% G -> A NA
LOC_Os04g41140.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os04g41150.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 94.896; most accessible tissue: Minghui63 panicle, score: 97.915
vg0424402289 (J) chr04 24402289 C T 99.40% 0.44% C -> T NA
LOC_Os04g41140.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os04g41150.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 94.994; most accessible tissue: Minghui63 panicle, score: 98.071
vg0424402315 (J) chr04 24402315 G A 98.90% 0.59% G -> A NA
LOC_Os04g41140.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41140.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.787; most accessible tissue: Minghui63 panicle, score: 98.268
vg0424402326 (J) chr04 24402326 G T 98.90% 0.57% G -> T NA
LOC_Os04g41140.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41140.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.223; most accessible tissue: Minghui63 panicle, score: 98.415
vg0424402352 (J) chr04 24402352 G Unkown 97.80% 1.42% G -> A NA
LOC_Os04g41140.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os04g41150.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 96.131; most accessible tissue: Minghui63 panicle, score: 98.892
vg0424402356 (J) chr04 24402356 C Unkown 97.90% 1.42% C -> T NA
LOC_Os04g41140.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os04g41150.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 96.168; most accessible tissue: Minghui63 panicle, score: 98.923
vg0424402382 (J) chr04 24402382 G Unkown 97.40% 2.56% G -> A NA
LOC_Os04g41140.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os04g41150.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 96.472; most accessible tissue: Minghui63 panicle, score: 99.087
vg0424402387 (J) chr04 24402387 G Unkown 97.40% 2.54% G -> A NA
LOC_Os04g41140.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os04g41150.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 96.524; most accessible tissue: Minghui63 panicle, score: 99.121
vg0424402392 (J) chr04 24402392 C Unkown 97.40% 2.48% C -> T NA
LOC_Os04g41140.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os04g41150.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 96.522; most accessible tissue: Zhenshan97 panicle, score: 99.125
vg0424402394 (J) chr04 24402394 G Unkown 97.40% 2.45% G -> A NA
LOC_Os04g41140.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os04g41150.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 96.549; most accessible tissue: Zhenshan97 panicle, score: 99.136
STR0424400923 (J) chr04 24400923 C A 87.70% 0.00% C -> A NA