15 variations found. LOC_Os07g42895 (expressed protein), ranging from 25,680,832 bp to 25,681,743 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0725680872 (J) | chr07 | 25680872 | TA | T | 99.50% | 0.00% | TA -> T,TAA,TAAA | NA |
LOC_Os07g42895.1 Alt: TAA| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os07g42885.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g42890.1 Alt: TAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g42900.1 Alt: TAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g42890.2 Alt: TAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g42895.1 Alt: TAAA| splice_region_variant&intron_variant LOW(snpEff) LOC_Os07g42885.1 Alt: TAAA| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g42890.1 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g42900.1 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g42890.2 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g42895.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff) LOC_Os07g42885.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g42890.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g42900.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g42890.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 |
| vg0725680876 (J) | chr07 | 25680876 | A | G | 96.70% | 0.00% | A -> G | NA |
LOC_Os07g42895.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os07g42885.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.412; most accessible tissue: Zhenshan97 flower, score: 61.362 |
| vg0725680883 (J) | chr07 | 25680883 | G | T | 62.30% | 0.23% | T -> G |
mr1070 (All); LR P-value: 2.44E-11;
mr1128 (All); LR P-value: 1.60E-10; mr1304 (All); LR P-value: 8.38E-20; mr1386 (All); LR P-value: 2.32E-14; mr1414 (All); LR P-value: 3.14E-31; mr1514 (All); LR P-value: 5.73E-08; mr1632 (All); LR P-value: 4.44E-26; mr1751 (All); LR P-value: 5.91E-11; mr1873 (All); LR P-value: 4.08E-40; mr1039_2 (All); LR P-value: 3.01E-27; mr1128_2 (All); LR P-value: 3.02E-13; mr1304_2 (All); LR P-value: 3.80E-24; mr1632_2 (All); LR P-value: 1.51E-33 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g42885.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.011; most accessible tissue: Zhenshan97 flower, score: 61.872 |
| vg0725680887 (J) | chr07 | 25680887 | A | T | 99.70% | 0.00% | A -> T | NA |
LOC_Os07g42885.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g42890.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g42900.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g42890.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g42895.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 37.281; most accessible tissue: Zhenshan97 flower, score: 61.872 |
| vg0725680919 (J) | chr07 | 25680919 | A | G | 68.00% | 25.84% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g42885.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.747; most accessible tissue: Zhenshan97 flower, score: 60.838 |
| vg0725680925 (J) | chr07 | 25680925 | AT | A | 65.40% | 0.11% | AT -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g42885.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 38.673; most accessible tissue: Zhenshan97 flower, score: 60.838 |
| vg0725680959 (J) | chr07 | 25680959 | T | A | 98.90% | 0.00% | T -> A | NA |
LOC_Os07g42885.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42890.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.565; most accessible tissue: Minghui63 flower, score: 57.706 |
| vg0725680995 (J) | chr07 | 25680995 | G | T | 97.60% | 0.00% | G -> T | NA |
LOC_Os07g42885.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42890.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.637; most accessible tissue: Minghui63 flower, score: 54.496 |
| vg0725681159 (J) | chr07 | 25681159 | GA | GAAA | 95.40% | 0.00% | GA -> GAAA,GAA,G ,GAAAA | NA |
LOC_Os07g42885.1 Alt: GAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42890.1 Alt: GAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: GAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: GAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: GAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42885.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42885.1 Alt: GAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.1 Alt: GAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: GAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: GAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: GAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42885.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.393; most accessible tissue: Minghui63 flower, score: 62.973 |
| vg0725681160 (J) | chr07 | 25681160 | A | G | 97.80% | 0.19% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g42885.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.393; most accessible tissue: Minghui63 flower, score: 62.973 |
| vg0725681375 (J) | chr07 | 25681375 | T | G | 62.30% | 0.34% | G -> T |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g42885.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.344; most accessible tissue: Minghui63 flower, score: 85.386 |
|
| vg0725681581 (J) | chr07 | 25681581 | T | A | 95.00% | 0.00% | T -> A | NA |
LOC_Os07g42885.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g42890.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42900.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42890.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g42895.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.862; most accessible tissue: Zhenshan97 panicle, score: 93.845 |
| vg0725681731 (J) | chr07 | 25681731 | G | T | 62.30% | 0.42% | T -> G |
mr1039 (All); LR P-value: 1.73E-25;
mr1070 (All); LR P-value: 1.24E-10; mr1128 (All); LR P-value: 3.77E-10; mr1304 (All); LR P-value: 3.22E-19; mr1386 (All); LR P-value: 9.64E-14; mr1414 (All); LR P-value: 9.63E-31; mr1514 (All); LR P-value: 5.21E-08; mr1632 (All); LR P-value: 2.75E-26; mr1751 (All); LR P-value: 3.25E-11; mr1873 (All); LR P-value: 3.31E-40; mr1039_2 (All); LR P-value: 2.60E-27; mr1128_2 (All); LR P-value: 1.96E-12; mr1304_2 (All); LR P-value: 1.91E-23; mr1632_2 (All); LR P-value: 1.06E-33 |
LOC_Os07g42895.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g42895.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 90.802; most accessible tissue: Zhenshan97 panicle, score: 97.400 |
| vg0725681740 (J) | chr07 | 25681740 | C | A | 96.70% | 0.00% | C -> A | NA |
LOC_Os07g42895.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.068; most accessible tissue: Zhenshan97 panicle, score: 97.512 |
| STR0725680930 (J) | chr07 | 25680930 | TTT | TT | 65.80% | 0.00% | TTT -> TT | NA |
|