403 variations found. LOC_Os07g01270 (transposon protein; putative; unclassified; expressed), ranging from 160,838 bp to 172,912 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0700160893 (J) | chr07 | 160893 | G | A | 94.20% | 5.25% | G -> A | NA |
LOC_Os07g01270.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g01270.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700160942 (J) | chr07 | 160942 | AT | Unkown | 86.50% | 12.04% | AT -> A | NA |
LOC_Os07g01260.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g01260.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01270.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700160945 (J) | chr07 | 160945 | A | C | 86.20% | 12.25% | A -> AC,C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: AC| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01260.2 Alt: AC| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01270.1 Alt: AC| intron_variant MODIFIER(snpEff) LOC_Os07g01260.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700160960 (J) | chr07 | 160960 | C | G | 86.10% | 12.36% | C -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700160977 (J) | chr07 | 160977 | A | C | 86.10% | 12.27% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700160980 (J) | chr07 | 160980 | T | TA | 86.20% | 12.27% | T -> TA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700160981 (J) | chr07 | 160981 | A | Unkown | 91.50% | 6.26% | A -> T | NA |
LOC_Os07g01260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g01260.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01270.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700160986 (J) | chr07 | 160986 | A | T | 93.20% | 5.84% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700160993 (J) | chr07 | 160993 | T | C | 75.40% | 2.24% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161005 (J) | chr07 | 161005 | GA | GAA | 98.80% | 0.51% | GA -> GAA,G | NA |
LOC_Os07g01260.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01260.2 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01260.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01270.1 Alt: G| intron_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161037 (J) | chr07 | 161037 | AG | CG | 58.60% | 21.56% | AG -> CG,A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01260.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01270.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os07g01260.1 Alt: CG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: CG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: CG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161050 (J) | chr07 | 161050 | C | A | 99.30% | 0.51% | C -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161071 (J) | chr07 | 161071 | A | Unkown | 96.70% | 1.99% | A -> G | NA |
LOC_Os07g01260.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g01260.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01270.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161073 (J) | chr07 | 161073 | G | T | 65.50% | 1.04% | G -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161093 (J) | chr07 | 161093 | C | T | 93.80% | 5.61% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161133 (J) | chr07 | 161133 | A | C | 56.20% | 31.85% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161134 (J) | chr07 | 161134 | G | A | 48.80% | 32.71% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161219 (J) | chr07 | 161219 | ACAG | A | 69.20% | 6.83% | ACAG -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161223 (J) | chr07 | 161223 | TGATTTG AA | T | 61.00% | 14.24% | TGATTTGAA -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161234 (J) | chr07 | 161234 | T | TA | 61.20% | 13.67% | T -> TA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161238 (J) | chr07 | 161238 | A | T | 49.60% | 7.00% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161280 (J) | chr07 | 161280 | G | A | 81.30% | 5.97% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161293 (J) | chr07 | 161293 | G | A | 83.60% | 6.39% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161357 (J) | chr07 | 161357 | G | A | 77.30% | 9.46% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01260.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01270.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700161392 (J) | chr07 | 161392 | C | T | 91.80% | 6.33% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01270.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01260.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
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