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Search Results:

15 variations found. LOC_Os07g38130 (polygalacturonase inhibitor 1 precursor; putative; expressed), ranging from 22,874,251 bp to 22,875,707 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
vg0722874347 (J) chr07 22874347 G GCAT 53.40% 0.06% G -> GCAT NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g38130.1 Alt: GCAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: GCAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 92.831; most accessible tissue: Minghui63 panicle, score: 99.892
vg0722874398 (J) chr07 22874398 A G 96.10% 0.00% A -> G
Awn_length (Jap_All); LR P-value: 7.13E-13;
mr1201 (Jap_All); LR P-value: 7.56E-06;
mr1274 (Jap_All); LR P-value: 1.97E-06;
mr1624 (Jap_All); LR P-value: 8.44E-09;
mr1057_2 (Jap_All); LR P-value: 5.91E-08;
mr1624_2 (Jap_All); LR P-value: 2.43E-09;
mr1733_2 (Jap_All); LR P-value: 2.50E-07;
mr1842_2 (Jap_All); LR P-value: 8.73E-06
LOC_Os07g38130.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.381; most accessible tissue: Minghui63 panicle, score: 99.876
vg0722874413 (J) chr07 22874413 T C 91.40% 0.00% T -> C
mr1376 (Ind_All); LR P-value: 2.10E-06;
mr1431 (Ind_All); LR P-value: 2.10E-06;
mr1820 (Ind_All); LR P-value: 5.90E-06;
mr1958 (Ind_All); LR P-value: 7.51E-06
LOC_Os07g38130.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.149; most accessible tissue: Minghui63 panicle, score: 99.866
vg0722874415 (J) chr07 22874415 C T 96.60% 0.00% C -> T
Awn_length (Jap_All); LR P-value: 2.61E-08;
mr1071 (Jap_All); LR P-value: 5.30E-06;
mr1203 (Jap_All); LR P-value: 8.22E-06;
mr1057_2 (Jap_All); LR P-value: 7.26E-07;
mr1624_2 (Jap_All); LR P-value: 7.68E-08;
mr1829_2 (Jap_All); LR P-value: 2.69E-06;
mr1842_2 (Jap_All); LR P-value: 8.74E-06
LOC_Os07g38130.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.171; most accessible tissue: Minghui63 panicle, score: 99.867
vg0722874422 (J) chr07 22874422 T A 99.00% 0.00% T -> A NA
LOC_Os07g38130.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.299; most accessible tissue: Minghui63 panicle, score: 99.873
vg0722874459 (J) chr07 22874459 C CT 94.70% 0.00% C -> CT NA
LOC_Os07g38130.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 94.020; most accessible tissue: Minghui63 panicle, score: 99.871
vg0722874621 (J) chr07 22874621 T C 59.90% 0.15% C -> T
mr1133 (All); LR P-value: 1.88E-18;
mr1659 (All); LR P-value: 4.93E-08;
mr1667 (All); LR P-value: 5.07E-12;
mr1149_2 (All); LR P-value: 1.83E-28;
mr1441_2 (All); LR P-value: 2.27E-26
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g38130.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 94.064; most accessible tissue: Minghui63 panicle, score: 99.857
vg0722874801 (J) chr07 22874801 G A 86.40% 0.00% G -> A
mr1304 (Ind_All); LR P-value: 1.88E-06;
mr1343 (All); LR P-value: 6.79E-07;
mr1376 (Ind_All); LR P-value: 2.26E-06;
mr1431 (Ind_All); LR P-value: 2.26E-06;
mr1530 (All); LR P-value: 4.64E-07;
mr1820 (Ind_All); LR P-value: 6.50E-06;
mr1830 (Ind_All); LR P-value: 9.48E-06;
mr1388_2 (All); LR P-value: 4.81E-09
LOC_Os07g38130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.073; most accessible tissue: Minghui63 panicle, score: 99.618
vg0722874861 (J) chr07 22874861 C T 58.80% 0.32% C -> T
mr1189 (All); LR P-value: 9.33E-06;
mr1531 (All); LR P-value: 9.36E-14;
mr1679 (Ind_All); LR P-value: 5.60E-06;
mr1796 (All); LR P-value: 7.13E-07;
mr1990 (All); LR P-value: 4.36E-07;
mr1679_2 (Ind_All); LR P-value: 5.46E-06;
mr1962_2 (Ind_All); LR P-value: 1.25E-08
LOC_Os07g38130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g38130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.861; most accessible tissue: Minghui63 panicle, score: 99.482
vg0722874941 (J) chr07 22874941 C T 94.10% 0.00% C -> T,G
mr1829 (All); LR P-value: 3.13E-08;
mr1585_2 (All); LR P-value: 3.33E-07;
mr1829_2 (All); LR P-value: 1.70E-10
LOC_Os07g38130.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os07g38140.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os07g38130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 90.845; most accessible tissue: Minghui63 panicle, score: 99.298
vg0722875224 (J) chr07 22875224 C A 99.90% 0.00% C -> A NA
LOC_Os07g38130.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os07g38140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 90.015; most accessible tissue: Minghui63 panicle, score: 99.212
vg0722875383 (J) chr07 22875383 C T 92.90% 0.00% C -> T,G NA
LOC_Os07g38130.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os07g38140.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os07g38130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.552; most accessible tissue: Minghui63 panicle, score: 99.462
vg0722875674 (J) chr07 22875674 G A 96.10% 0.00% G -> A
Awn_length (Jap_All); LR P-value: 7.13E-13;
mr1201 (Jap_All); LR P-value: 7.56E-06;
mr1274 (Jap_All); LR P-value: 1.97E-06;
mr1624 (Jap_All); LR P-value: 8.44E-09;
mr1057_2 (Jap_All); LR P-value: 5.91E-08;
mr1624_2 (Jap_All); LR P-value: 2.43E-09;
mr1733_2 (Jap_All); LR P-value: 2.50E-07;
mr1842_2 (Jap_All); LR P-value: 8.73E-06
LOC_Os07g38130.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38150.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 94.580; most accessible tissue: Minghui63 panicle, score: 99.888
vg0722875693 (J) chr07 22875693 T A 94.10% 0.00% T -> A
mr1829 (All); LR P-value: 3.13E-08;
mr1585_2 (All); LR P-value: 3.33E-07;
mr1829_2 (All); LR P-value: 1.70E-10
LOC_Os07g38130.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38150.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 95.393; most accessible tissue: Minghui63 panicle, score: 99.911
STR0722874348 (J) chr07 22874348 CATCATC CATC 47.30% 0.00% CATC -> CATCATC NA