23 variations found. LOC_Os01g66720 (NADP-dependent oxidoreductase; putative; expressed), ranging from 38,752,610 bp to 38,754,970 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Color | Explain | Details |
|---|---|---|
| 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. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| vg0138752753 (J) | chr01 | 38752753 | C | T | 59.50% | 0.49% | C -> T |
LOC_Os01g66720.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g66720.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 97.403; most accessible tissue: Zhenshan97 panicle, score: 99.024 |
|
| vg0138753354 (J) | chr01 | 38753354 | G | A | 98.00% | 0.00% | G -> A | NA |
LOC_Os01g66710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 50.552; most accessible tissue: Zhenshan97 flower, score: 62.865 |
| vg0138753386 (J) | chr01 | 38753386 | C | A | 98.00% | 0.00% | C -> A | NA |
LOC_Os01g66710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.016; most accessible tissue: Minghui63 panicle, score: 56.842 |
| vg0138753405 (J) | chr01 | 38753405 | A | G | 60.40% | 0.00% | G -> A |
mr1457 (All); LR P-value: 1.17E-08;
mr1458 (All); LR P-value: 3.26E-43; mr1720 (All); LR P-value: 8.56E-12; mr1841 (All); LR P-value: 2.26E-23; mr1862 (All); LR P-value: 4.27E-24; mr1945 (All); LR P-value: 7.56E-10; mr1458_2 (All); LR P-value: 1.20E-50; mr1571_2 (All); LR P-value: 2.93E-32; mr1672_2 (Jap_All); LR P-value: 3.17E-06; mr1720_2 (All); LR P-value: 2.87E-16; mr1946_2 (Jap_All); LR P-value: 9.26E-07; mr1948_2 (Jap_All); LR P-value: 9.26E-07 |
LOC_Os01g66710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 39.282; most accessible tissue: Minghui63 panicle, score: 53.770 |
| vg0138753428 (J) | chr01 | 38753428 | G | T | 79.80% | 0.44% | G -> T | NA |
LOC_Os01g66710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66730.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 38.669; most accessible tissue: Callus, score: 72.221 |
| vg0138753539 (J) | chr01 | 38753539 | CT | CTT | 97.20% | 0.00% | CT -> CTT,C | NA |
LOC_Os01g66710.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66730.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 38.320; most accessible tissue: Callus, score: 72.221 |
| vg0138753562 (J) | chr01 | 38753562 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os01g66710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g66730.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66730.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66720.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 36.578; most accessible tissue: Callus, score: 72.221 |
| vg0138753655 (J) | chr01 | 38753655 | C | G | 99.70% | 0.00% | C -> G | NA |
LOC_Os01g66710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g66730.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66730.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66720.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 30.430; most accessible tissue: Minghui63 panicle, score: 62.157 |
| vg0138753663 (J) | chr01 | 38753663 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os01g66710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g66730.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66730.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66720.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 30.137; most accessible tissue: Minghui63 panicle, score: 59.629 |
| vg0138753723 (J) | chr01 | 38753723 | C | T | 95.20% | 0.00% | C -> T | NA |
LOC_Os01g66710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66730.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 33.956; most accessible tissue: Callus, score: 74.601 |
| vg0138753757 (J) | chr01 | 38753757 | G | A | 96.30% | 0.00% | G -> A | NA |
LOC_Os01g66710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 34.413; most accessible tissue: Callus, score: 74.601 |
| vg0138753955 (J) | chr01 | 38753955 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os01g66720.1 Alt: T| stop_gained HIGH(snpEff)
LOC_Os01g66710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66730.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 45.511; most accessible tissue: Callus, score: 84.070 |
| vg0138754197 (J) | chr01 | 38754197 | T | C | 98.00% | 0.00% | T -> C | NA |
LOC_Os01g66710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.174; most accessible tissue: Callus, score: 85.066 |
| vg0138754243 (J) | chr01 | 38754243 | AATTAAG ATAGATT | A | 99.70% | 0.00% | AATTAAGATA GATT -> A | NA |
LOC_Os01g66710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g66730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66730.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g66720.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 56.667; most accessible tissue: Callus, score: 85.066 |
| vg0138754405 (J) | chr01 | 38754405 | A | G | 54.80% | 0.49% | A -> G |
LOC_Os01g66710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66730.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 64.323; most accessible tissue: Zhenshan97 panicle, score: 76.605 |
|
| vg0138754447 (J) | chr01 | 38754447 | G | C | 97.80% | 0.00% | G -> C | NA |
LOC_Os01g66710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.468; most accessible tissue: Callus, score: 83.786 |
| vg0138754536 (J) | chr01 | 38754536 | G | C | 95.20% | 0.00% | G -> C | NA |
LOC_Os01g66720.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.173; most accessible tissue: Callus, score: 83.786 |
| vg0138754556 (J) | chr01 | 38754556 | G | A | 79.80% | 0.49% | G -> A | NA |
LOC_Os01g66720.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g66720.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 75.286; most accessible tissue: Zhenshan97 panicle, score: 84.374 |
| vg0138754768 (J) | chr01 | 38754768 | T | G | 79.80% | 0.49% | T -> G | NA |
LOC_Os01g66720.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g66720.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 72.901; most accessible tissue: Callus, score: 81.248 |
| vg0138754845 (J) | chr01 | 38754845 | G | T | 67.60% | 0.00% | T -> G |
mr1027 (All); LR P-value: 6.67E-67;
mr1134 (All); LR P-value: 3.96E-83; mr1135 (All); LR P-value: 1.69E-84; mr1256 (All); LR P-value: 2.59E-29; mr1375 (All); LR P-value: 2.60E-24; mr1504 (All); LR P-value: 1.20E-92; mr1538 (All); LR P-value: 3.02E-69; mr1670 (All); LR P-value: 2.51E-35; mr1672 (All); LR P-value: 1.90E-93; mr1767 (All); LR P-value: 1.10E-17; mr1830 (All); LR P-value: 1.13E-15; mr1909 (All); LR P-value: 1.79E-13; mr1921 (All); LR P-value: 2.50E-10; mr1933 (All); LR P-value: 7.77E-15; mr1281_2 (All); LR P-value: 3.09E-18; mr1504_2 (All); LR P-value: 6.17E-87; mr1538_2 (All); LR P-value: 7.40E-108; mr1541_2 (All); LR P-value: 6.70E-38; mr1672_2 (All); LR P-value: 2.53E-118; mr1672_2 (Jap_All); LR P-value: 3.17E-06; mr1946_2 (Jap_All); LR P-value: 9.26E-07; mr1948_2 (Jap_All); LR P-value: 9.26E-07 |
LOC_Os01g66720.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.029; most accessible tissue: Zhenshan97 panicle, score: 81.752 |
| vg0138754905 (J) | chr01 | 38754905 | TCTTAAC ATGTTCA AATTATA C | T | 79.80% | 0.49% | TCTTAACATG TTCAAATTAT AC -> T | NA |
LOC_Os01g66720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 65.655; most accessible tissue: Zhenshan97 panicle, score: 81.752 |
| vg0138754938 (J) | chr01 | 38754938 | GTTCAAT TCGCTCA CTCAATA CCAGTGA AAATATT AATTACC A | G | 95.30% | 0.00% | GTTCAATTCG CTCACTCAAT ACCAGTGAAA ATATTAATTA CCA -> G | NA |
LOC_Os01g66720.1 Alt: G| splice_region_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g66720.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66740.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720-LOC_Os01g66730 Alt: G| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66720.1 Alt: G| non_coding_transcript_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.957; most accessible tissue: Callus, score: 80.690 |
| vg0138754947 (J) | chr01 | 38754947 | A | G | 60.40% | 4.15% | G -> A |
LOC_Os01g66720.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g66740.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g66730.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 66.545; most accessible tissue: Callus, score: 80.690 |