41 variations found. LOC_Os06g35340 (retrotransposon; putative; centromere-specific), ranging from 20,601,609 bp to 20,603,342 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602194 (J) | chr06 | 20602194 | G | A | 97.80% | 1.18% | G -> A | NA |
LOC_Os06g35340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.088; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0620602238 (J) | chr06 | 20602238 | G | A | 90.70% | 1.14% | G -> A | NA |
LOC_Os06g35340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.088; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0620602250 (J) | chr06 | 20602250 | T | G | 85.50% | 1.25% | G -> T | NA |
LOC_Os06g35340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.088; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0620602260 (J) | chr06 | 20602260 | G | A | 81.70% | 1.16% | G -> A,T | NA |
LOC_Os06g35340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g35340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.088; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0620602295 (J) | chr06 | 20602295 | G | A | 97.40% | 1.14% | G -> A | NA |
LOC_Os06g35340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.088; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0620602324 (J) | chr06 | 20602324 | G | A | 82.60% | 1.16% | G -> A | NA |
LOC_Os06g35340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 8.197; most accessible tissue: Minghui63 root, score: 10.708 |
| vg0620602332 (J) | chr06 | 20602332 | T | C | 74.80% | 1.25% | T -> C | NA |
LOC_Os06g35340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 8.100; most accessible tissue: Minghui63 root, score: 10.708 |
| vg0620602381 (J) | chr06 | 20602381 | C | T | 98.60% | 1.18% | C -> T | NA |
LOC_Os06g35340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 8.320; most accessible tissue: Minghui63 flower, score: 11.139 |
| vg0620602383 (J) | chr06 | 20602383 | G | A | 97.40% | 1.14% | G -> A | NA |
LOC_Os06g35340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 8.320; most accessible tissue: Minghui63 flower, score: 11.139 |
| vg0620602415 (J) | chr06 | 20602415 | A | G | 97.40% | 1.14% | A -> G | NA |
LOC_Os06g35340.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.275; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0620602558 (J) | chr06 | 20602558 | A | G | 13.20% | 17.80% | A -> G | NA |
LOC_Os06g35340.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 15.478; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg0620602566 (J) | chr06 | 20602566 | A | G | 98.30% | 1.18% | A -> G | NA |
LOC_Os06g35340.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 15.673; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg0620602571 (J) | chr06 | 20602571 | C | T | 97.40% | 1.14% | C -> T | NA |
LOC_Os06g35340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 15.741; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg0620602624 (J) | chr06 | 20602624 | G | A | 97.30% | 1.16% | G -> A |
mr1024_2 (Jap_All); LMM P-value: 2.79E-06; LR P-value: 2.79E-06;
mr1037_2 (Jap_All); LMM P-value: 8.74E-07; LR P-value: 3.33E-07; mr1291_2 (Jap_All); LR P-value: 4.47E-06; mr1367_2 (Jap_All); LMM P-value: 6.35E-06; LR P-value: 6.35E-06; mr1565_2 (Jap_All); LR P-value: 1.65E-06; mr1726_2 (Jap_All); LR P-value: 8.29E-06; mr1827_2 (Jap_All); LR P-value: 2.56E-07 |
LOC_Os06g35340.1 Alt: A/splice_acceptor_variant(CooVar)
LOC_Os06g35340.1 Alt: DEL/splice_acceptor_variant(CooVar) The average chromatin accessibility score: 16.440; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg0620602637 (J) | chr06 | 20602637 | C | T | 97.40% | 1.14% | C -> T | NA |
LOC_Os06g35340.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 17.216; most accessible tissue: Zhenshan97 root, score: 23.888 |
| vg0620602649 (J) | chr06 | 20602649 | C | T | 97.40% | 1.14% | C -> T | NA |
LOC_Os06g35340.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 17.216; most accessible tissue: Zhenshan97 root, score: 23.888 |
| vg0620602697 (J) | chr06 | 20602697 | A | G | 97.40% | 1.14% | A -> G | NA |
LOC_Os06g35340.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.484; most accessible tissue: Minghui63 young leaf, score: 26.082 |
| vg0620602722 (J) | chr06 | 20602722 | G | A | 97.20% | 1.21% | G -> A |
mr1024_2 (Jap_All); LMM P-value: 2.79E-06; LR P-value: 2.79E-06;
mr1037_2 (Jap_All); LMM P-value: 8.74E-07; LR P-value: 3.33E-07; mr1291_2 (Jap_All); LR P-value: 4.47E-06; mr1367_2 (Jap_All); LMM P-value: 6.35E-06; LR P-value: 6.35E-06; mr1565_2 (Jap_All); LR P-value: 1.65E-06; mr1726_2 (Jap_All); LR P-value: 8.29E-06; mr1827_2 (Jap_All); LR P-value: 2.56E-07 |
LOC_Os06g35340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 18.866; most accessible tissue: Minghui63 flag leaf, score: 25.154 |
| vg0620602800 (J) | chr06 | 20602800 | A | G | 66.10% | 1.25% | G -> A | NA |
LOC_Os06g35340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 18.528; most accessible tissue: Zhenshan97 root, score: 25.639 |
| vg0620602852 (J) | chr06 | 20602852 | C | G | 0.70% | 53.24% | C -> G | NA |
LOC_Os06g35340.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.595; most accessible tissue: Minghui63 flag leaf, score: 22.094 |
| vg0620602899 (J) | chr06 | 20602899 | C | A | 4.10% | 42.11% | C -> A | NA |
LOC_Os06g35340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.051; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg0620602920 (J) | chr06 | 20602920 | G | T | 75.40% | 2.67% | G -> T | NA |
LOC_Os06g35340.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.490; most accessible tissue: Minghui63 flag leaf, score: 17.725 |
| vg0620602925 (J) | chr06 | 20602925 | G | C | 96.00% | 1.21% | G -> C | NA |
LOC_Os06g35340.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.336; most accessible tissue: Minghui63 flag leaf, score: 17.373 |
| vg0620602928 (J) | chr06 | 20602928 | T | C | 97.00% | 1.16% | T -> C | NA |
LOC_Os06g35340.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.336; most accessible tissue: Minghui63 flag leaf, score: 17.373 |
| vg0620602930 (J) | chr06 | 20602930 | A | G | 98.60% | 1.18% | A -> G | NA |
LOC_Os06g35340.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.336; most accessible tissue: Minghui63 flag leaf, score: 17.373 |
| vg0620602939 (J) | chr06 | 20602939 | C | T | 97.20% | 1.21% | C -> T | NA |
LOC_Os06g35340.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.084; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0620602945 (J) | chr06 | 20602945 | A | G | 97.40% | 1.14% | A -> G | NA |
LOC_Os06g35340.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.652; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0620602949 (J) | chr06 | 20602949 | G | A | 97.40% | 1.14% | G -> A | NA |
LOC_Os06g35340.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.573; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0620602961 (J) | chr06 | 20602961 | C | T | 82.60% | 1.18% | C -> T | NA |
LOC_Os06g35340.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.636; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0620602980 (J) | chr06 | 20602980 | AAAACGC CGT | A | 97.20% | 1.21% | AAAACGCCGT -> A | NA |
LOC_Os06g35340.1 Alt: A| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.346; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0620602984 (J) | chr06 | 20602984 | C | T | 97.60% | 1.12% | C -> T | NA |
LOC_Os06g35340.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.346; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0620602988 (J) | chr06 | 20602988 | G | A | 96.40% | 1.14% | G -> A | NA |
LOC_Os06g35340.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.279; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0620603030 (J) | chr06 | 20603030 | T | A | 97.20% | 1.21% | T -> A | NA |
LOC_Os06g35340.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 11.128; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0620603048 (J) | chr06 | 20603048 | C | T | 85.50% | 1.23% | T -> C | NA |
LOC_Os06g35340.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.317; most accessible tissue: Minghui63 flag leaf, score: 15.205 |
| vg0620603060 (J) | chr06 | 20603060 | G | A | 85.50% | 1.23% | A -> G | NA |
LOC_Os06g35340.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.028; most accessible tissue: Minghui63 flag leaf, score: 14.810 |
| vg0620603068 (J) | chr06 | 20603068 | C | G | 74.90% | 1.23% | C -> G | NA |
LOC_Os06g35340.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.910; most accessible tissue: Minghui63 flag leaf, score: 14.810 |
| vg0620603073 (J) | chr06 | 20603073 | G | A | 82.70% | 1.18% | G -> A | NA |
LOC_Os06g35340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.040; most accessible tissue: Minghui63 flag leaf, score: 12.986 |
| vg0620603108 (J) | chr06 | 20603108 | G | A | 97.60% | 1.23% | G -> A | NA |
LOC_Os06g35340.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.749; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0620603154 (J) | chr06 | 20603154 | G | A | 97.40% | 1.14% | G -> A,C | NA |
LOC_Os06g35340.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os06g35340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.229; most accessible tissue: Minghui63 flower, score: 9.270 |
| vg0620603162 (J) | chr06 | 20603162 | G | A | 90.70% | 1.23% | G -> A | NA |
LOC_Os06g35340.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.229; most accessible tissue: Minghui63 flower, score: 9.270 |
| vg0620603335 (J) | chr06 | 20603335 | AG | A | 84.90% | 1.71% | A -> AG,G | NA |
LOC_Os06g35340.1 Alt: AG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os06g35340.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os06g35340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.229; most accessible tissue: Minghui63 flower, score: 9.270 |