81 variations found. LOC_Os04g54310 (expressed protein), ranging from 32,336,346 bp to 32,337,872 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0432336368 (J) | chr04 | 32336368 | A | G | 94.70% | 3.32% | A -> G | NA |
LOC_Os04g54310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g54310.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 93.744; most accessible tissue: Minghui63 flower, score: 98.415 |
| vg0432336374 (J) | chr04 | 32336374 | TGCCGCT GCA | T | 98.70% | 0.00% | TGCCGCTGCA -> T | NA |
LOC_Os04g54310.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 93.741; most accessible tissue: Minghui63 flower, score: 98.422 |
| vg0432336397 (J) | chr04 | 32336397 | C | T | 97.50% | 0.00% | C -> T | NA |
LOC_Os04g54310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.878; most accessible tissue: Minghui63 flower, score: 98.499 |
| vg0432336427 (J) | chr04 | 32336427 | A | Unkown | 97.80% | 1.02% | A -> C | NA |
LOC_Os04g54310.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os04g54300.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54320.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.290; most accessible tissue: Minghui63 flower, score: 98.485 |
| vg0432336496 (J) | chr04 | 32336496 | G | GGTCACC AGTGTTG TGTGA | 93.70% | 2.29% | G -> GGTCACCAGT GTTGTGTGA | NA |
LOC_Os04g54310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g54310.1 Alt: GGTCACCAGTGTTGTGTGA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 94.487; most accessible tissue: Minghui63 flower, score: 98.025 |
| vg0432336509 (J) | chr04 | 32336509 | G | Unkown | 79.50% | 16.84% | G -> T | NA |
LOC_Os04g54310.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os04g54300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.341; most accessible tissue: Minghui63 flower, score: 97.915 |
| vg0432336518 (J) | chr04 | 32336518 | C | T | 78.30% | 18.37% | C -> T | NA |
LOC_Os04g54310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g54310.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 94.372; most accessible tissue: Minghui63 flower, score: 97.920 |
| vg0432336540 (J) | chr04 | 32336540 | G | GATAGTT C | 72.70% | 21.20% | G -> GATAGTTC | NA |
LOC_Os04g54310.1 Alt: GATAGTTC| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os04g54310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 95.761; most accessible tissue: Minghui63 flower, score: 98.509 |
| vg0432336548 (J) | chr04 | 32336548 | G | C | 97.80% | 0.00% | G -> C | NA |
LOC_Os04g54310.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 96.011; most accessible tissue: Minghui63 flower, score: 98.619 |
| vg0432336574 (J) | chr04 | 32336574 | C | Unkown | 99.50% | 0.25% | C -> T | NA |
LOC_Os04g54310.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os04g54300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.798; most accessible tissue: Minghui63 flower, score: 98.931 |
| vg0432336599 (J) | chr04 | 32336599 | T | A | 94.50% | 0.80% | T -> A | NA |
LOC_Os04g54310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g54310.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 96.049; most accessible tissue: Minghui63 flower, score: 99.045 |
| vg0432336602 (J) | chr04 | 32336602 | T | C | 97.60% | 0.38% | T -> C | NA |
LOC_Os04g54310.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g54310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 96.052; most accessible tissue: Minghui63 flower, score: 99.038 |
| vg0432336612 (J) | chr04 | 32336612 | C | T | 63.10% | 32.31% | C -> T | NA |
LOC_Os04g54310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g54310.1 Alt: T| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 96.138; most accessible tissue: Minghui63 flower, score: 99.066 |
| vg0432336613 (J) | chr04 | 32336613 | G | A | 98.10% | 0.68% | G -> A | NA |
LOC_Os04g54310.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g54310.1 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 96.146; most accessible tissue: Minghui63 flower, score: 99.073 |
| vg0432336625 (J) | chr04 | 32336625 | A | C | 97.20% | 2.03% | A -> C | NA |
LOC_Os04g54300.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g54320.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54310.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 96.287; most accessible tissue: Minghui63 flower, score: 99.156 |
| vg0432336626 (J) | chr04 | 32336626 | G | A | 97.00% | 2.48% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g54300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54320.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54310.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.287; most accessible tissue: Minghui63 flower, score: 99.156 |
| vg0432336659 (J) | chr04 | 32336659 | AACTGCA AACATG | Unkown | 91.50% | 7.60% | AACTGCAAAC ATG -> A | NA |
LOC_Os04g54300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g54320.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54310.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.668; most accessible tissue: Minghui63 flower, score: 99.278 |
| vg0432336680 (J) | chr04 | 32336680 | A | G | 77.30% | 20.95% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g54300.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54320.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54310.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.253; most accessible tissue: Minghui63 flower, score: 99.325 |
| vg0432336681 (J) | chr04 | 32336681 | AAACTC | A | 69.30% | 27.74% | AAACTC -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g54300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54320.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54310.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.253; most accessible tissue: Minghui63 flower, score: 99.326 |
| vg0432336690 (J) | chr04 | 32336690 | G | T | 97.20% | 2.52% | G -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g54300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54310.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.281; most accessible tissue: Minghui63 flower, score: 99.358 |
| vg0432336696 (J) | chr04 | 32336696 | C | CG | 89.70% | 9.29% | C -> CG | NA |
LOC_Os04g54300.1 Alt: CG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g54320.1 Alt: CG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.1 Alt: CG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.3 Alt: CG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.2 Alt: CG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54310.1 Alt: CG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 98.370; most accessible tissue: Minghui63 flower, score: 99.398 |
| vg0432336697 (J) | chr04 | 32336697 | GA | GAA | 95.50% | 2.71% | GA -> G,GAA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g54300.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54320.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.3 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.2 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54310.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54300.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54320.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54310.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.370; most accessible tissue: Minghui63 flower, score: 99.399 |
| vg0432336698 (J) | chr04 | 32336698 | A | G | 76.10% | 20.95% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g54300.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54320.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54310.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.368; most accessible tissue: Minghui63 flower, score: 99.397 |
| vg0432336707 (J) | chr04 | 32336707 | A | T | 70.00% | 26.58% | A -> T,AT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g54300.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54320.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.3 Alt: AT| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54330.2 Alt: AT| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g54310.1 Alt: AT| intron_variant MODIFIER(snpEff) LOC_Os04g54300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54310.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.479; most accessible tissue: Minghui63 flower, score: 99.459 |
| vg0432336709 (J) | chr04 | 32336709 | G | T | 68.60% | 19.17% | G -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g54300.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54330.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g54310.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.475; most accessible tissue: Minghui63 flower, score: 99.453 |
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