23 variations found. LOC_Os01g33180 (hypothetical protein), ranging from 18,270,446 bp to 18,270,725 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270461 (J) | chr01 | 18270461 | G | A | 60.90% | 1.90% | A -> G |
mr1021 (All); LR P-value: 3.24E-19;
mr1092 (All); LR P-value: 1.07E-44; mr1228 (All); LR P-value: 5.85E-15; mr1242 (All); LR P-value: 5.36E-19; mr1519 (All); LR P-value: 5.45E-51; mr1744 (All); LR P-value: 6.15E-12; mr1299_2 (All); LR P-value: 5.35E-08; mr1379_2 (All); LR P-value: 4.88E-09; mr1519_2 (All); LR P-value: 1.52E-52; mr1700_2 (All); LR P-value: 9.79E-08; mr1727_2 (All); LR P-value: 2.03E-07; mr1840_2 (All); LR P-value: 3.84E-06 |
LOC_Os01g33180.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g33180.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 54.568; most accessible tissue: Minghui63 young leaf, score: 76.820 |
| vg0118270473 (J) | chr01 | 18270473 | T | A | 99.60% | 0.00% | T -> A | NA |
LOC_Os01g33180.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os01g33160.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g33190.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.726; most accessible tissue: Minghui63 young leaf, score: 75.479 |
| vg0118270475 (J) | chr01 | 18270475 | C | T | 87.80% | 0.00% | C -> T |
LOC_Os01g33180.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 53.812; most accessible tissue: Minghui63 young leaf, score: 75.479 |
|
| vg0118270477 (J) | chr01 | 18270477 | C | T | 99.20% | 0.00% | C -> A,T | NA |
LOC_Os01g33180.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g33180.1 Alt: A| missense_variant MODERATE(snpEff) LOC_Os01g33160.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g33190.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.769; most accessible tissue: Minghui63 young leaf, score: 75.006 |
| vg0118270489 (J) | chr01 | 18270489 | G | A | 97.90% | 0.00% | G -> A | NA |
LOC_Os01g33180.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 53.456; most accessible tissue: Minghui63 young leaf, score: 75.479 |
| vg0118270500 (J) | chr01 | 18270500 | GAGTAGA ATCATCT CTCAAAC ACCAATG GAGGTTG CGGTGCG GGAGATT GCTACGT ACTGGTT CGAGAAC CAGCGAG CA | G | 99.80% | 0.00% | GAGTAGAATC ATCTCTCAAA CACCAATGGA GGTTGCGGTG CGGGAGATTG CTACGTACTG GTTCGAGAAC CAGCGAGCA -> G | NA |
LOC_Os01g33180.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)
LOC_Os01g33160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g33190.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 52.891; most accessible tissue: Minghui63 young leaf, score: 74.007 |
| vg0118270517 (J) | chr01 | 18270517 | A | G | 74.30% | 20.02% | A -> G | NA |
LOC_Os01g33180.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g33180.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 53.561; most accessible tissue: Minghui63 young leaf, score: 73.490 |
| vg0118270532 (J) | chr01 | 18270532 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os01g33180.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os01g33160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g33190.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 55.403; most accessible tissue: Minghui63 young leaf, score: 74.007 |
| vg0118270540 (J) | chr01 | 18270540 | CGG | C | 99.10% | 0.00% | CGG -> C | NA |
LOC_Os01g33180.1 Alt: C| frameshift_variant HIGH(snpEff)
LOC_Os01g33160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 55.174; most accessible tissue: Minghui63 young leaf, score: 74.514 |
| vg0118270542 (J) | chr01 | 18270542 | G | A | 87.70% | 0.00% | G -> A | NA |
LOC_Os01g33180.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 55.370; most accessible tissue: Minghui63 young leaf, score: 74.514 |
| vg0118270545 (J) | chr01 | 18270545 | GATTGCT ACGTACT GGTTCGA GAACCAG CGAGCAA GTAGAAT CATCTCT CGAACAC CAATGGA GGTTGCG GTGCGGG AGATTGC TACGTAC TGGTTCA AGAACC | Unkown | 99.30% | 0.00% | GATTGCTACG TACTGGTTCG AGAACCAGCG AGCAAGTAGA ATCATCTCTC GAACACCAAT GGAGGTTGCG GTGCGGGAGA TTGCTACGTA CTGGTTCAAG AACC -> G | NA |
LOC_Os01g33180.1 Alt: G| frameshift_variant HIGH(snpEff)
LOC_Os01g33160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.798; most accessible tissue: Minghui63 young leaf, score: 74.514 |
| vg0118270553 (J) | chr01 | 18270553 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os01g33180.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g33160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g33190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.795; most accessible tissue: Minghui63 young leaf, score: 74.514 |
| vg0118270578 (J) | chr01 | 18270578 | A | G | 38.90% | 27.36% | A -> G,AGTAGAAT CATCCCTCGA ACACCAATGG AGGTTGTGGT GCGGGAGATT GCTACGTACT AGTTCGAGAA CCAGCGAGCG | NA |
LOC_Os01g33180.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g33180.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g33180.1 Alt: AGTAGAATCATCCCTCGAACACCAATGGAGGTTGTGGTGCGGGAGATTGCTACGTACTAGTTCGAGAACCAGCGAGCG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 52.913; most accessible tissue: Minghui63 young leaf, score: 74.514 |
| vg0118270591 (J) | chr01 | 18270591 | T | C | 97.30% | 0.53% | T -> C | NA |
LOC_Os01g33180.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g33180.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 53.336; most accessible tissue: Minghui63 young leaf, score: 74.514 |
| vg0118270605 (J) | chr01 | 18270605 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os01g33180.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g33160.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g33190.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 52.724; most accessible tissue: Minghui63 young leaf, score: 71.839 |
| vg0118270613 (J) | chr01 | 18270613 | C | T | 98.90% | 0.00% | C -> T | NA |
LOC_Os01g33180.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 52.105; most accessible tissue: Minghui63 young leaf, score: 71.254 |
| vg0118270621 (J) | chr01 | 18270621 | GAGATTG CTACGTA CTGGTTC AAGAACC | Unkown | 63.80% | 33.45% | GAGATTGCTA CGTACTGGTT CAAGAACC -> G | NA |
LOC_Os01g33180.1 Alt: G| inframe_deletion MODERATE(snpEff)
LOC_Os01g33160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g33190.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 51.804; most accessible tissue: Minghui63 young leaf, score: 70.038 |
| vg0118270631 (J) | chr01 | 18270631 | C | T | 63.50% | 27.93% | C -> T,CGTACTGG TTCAAGAACC AGATTGCTAC GTACTGGTTC GAGAACCAGC GAGCGAGTAG AATCATCTCT CGAACACCAA TGGAGGTTGC GGTGCGGAAG ATTGCTAT | NA |
LOC_Os01g33180.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g33180.1 Alt: CGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTAT| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os01g33180.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 51.295; most accessible tissue: Minghui63 young leaf, score: 70.038 |
| vg0118270638 (J) | chr01 | 18270638 | G | A | 77.30% | 0.00% | G -> A | NA |
LOC_Os01g33180.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 52.524; most accessible tissue: Minghui63 young leaf, score: 70.038 |
| vg0118270643 (J) | chr01 | 18270643 | A | T | 97.70% | 0.00% | A -> T | NA |
LOC_Os01g33180.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 52.848; most accessible tissue: Minghui63 young leaf, score: 70.655 |
| vg0118270700 (J) | chr01 | 18270700 | G | A | 79.00% | 8.51% | G -> A,GAACACCA ATGGAGGTTG CGGTGCGGAA GATTGCTATG TACTGGTTCA AGAACCAGAT TGCTACGTAC TGGTTCGAGA ACCAGCGAGC TAGTAGAATC ATCTCTCA | NA |
LOC_Os01g33180.1 Alt: GAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTATGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCTAGTAGAATCATCTCTCA| disruptive_inframe_insertion MODERATE(snpEff)
LOC_Os01g33160.1 Alt: GAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTATGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCTAGTAGAATCATCTCTCA| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g33190.1 Alt: GAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTATGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCTAGTAGAATCATCTCTCA| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g33180.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os01g33180.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 54.279; most accessible tissue: Minghui63 young leaf, score: 70.655 |
| vg0118270711 (J) | chr01 | 18270711 | G | A | 98.50% | 0.00% | G -> A | NA |
LOC_Os01g33180.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 54.099; most accessible tissue: Minghui63 young leaf, score: 70.038 |
| vg0118270723 (J) | chr01 | 18270723 | C | T | 56.20% | 0.66% | T -> C |
mr1519 (All); LR P-value: 6.15E-48;
mr1647 (All); LR P-value: 1.01E-31; mr1731 (All); LR P-value: 2.38E-24; mr1040_2 (All); LR P-value: 1.11E-15; mr1087_2 (All); LR P-value: 1.49E-71; mr1211_2 (All); LR P-value: 2.71E-55; mr1281_2 (All); LR P-value: 7.39E-18; mr1379_2 (All); LR P-value: 2.07E-09; mr1398_2 (All); LR P-value: 6.75E-10; mr1519_2 (All); LR P-value: 1.18E-48; mr1537_2 (All); LR P-value: 8.47E-11; mr1568_2 (All); LR P-value: 9.56E-07; mr1581_2 (All); LR P-value: 1.87E-18; mr1727_2 (All); LR P-value: 6.95E-07; mr1770_2 (All); LR P-value: 9.57E-13; mr1783_2 (All); LR P-value: 1.05E-07; mr1804_2 (All); LR P-value: 2.41E-07; mr1916_2 (All); LR P-value: 4.27E-25 |
LOC_Os01g33180.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g33180.1 Alt: C| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar) The average chromatin accessibility score: 54.205; most accessible tissue: Minghui63 young leaf, score: 71.839 |