38 variations found. LOC_Os03g55990 (homeobox domain containing protein; expressed), ranging from 31,869,146 bp to 31,871,521 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0331869187 (J) | chr03 | 31869187 | G | GCCATCC | 95.20% | 0.00% | G -> GCCATCC | NA |
LOC_Os03g55990.1 Alt: GCCATCC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55990.3 Alt: GCCATCC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55990.2 Alt: GCCATCC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55980.1 Alt: GCCATCC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.164; most accessible tissue: Zhenshan97 flower, score: 99.578 |
| vg0331869199 (J) | chr03 | 31869199 | C | Unkown | 99.80% | 0.19% | C -> CAT,G | NA |
LOC_Os03g55990.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g55990.3 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55990.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55980.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g55990.1 Alt: CAT| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55990.3 Alt: CAT| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55990.2 Alt: CAT| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55980.1 Alt: CAT| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.204; most accessible tissue: Zhenshan97 flower, score: 99.594 |
| vg0331869201 (J) | chr03 | 31869201 | CGG | Unkown | 99.80% | 0.19% | CGG -> AGG,C | NA |
LOC_Os03g55990.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g55990.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55990.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55980.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g55990.1 Alt: AGG| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55990.3 Alt: AGG| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55990.2 Alt: AGG| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55980.1 Alt: AGG| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.205; most accessible tissue: Zhenshan97 flower, score: 99.592 |
| vg0331869281 (J) | chr03 | 31869281 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os03g55990.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)
LOC_Os03g55990.3 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os03g55990.2 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os03g55990.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55990.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55990.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g55980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.958; most accessible tissue: Zhenshan97 flower, score: 99.461 |
| vg0331869466 (J) | chr03 | 31869466 | T | C | 56.70% | 0.00% | C -> T |
mr1276 (All); LR P-value: 2.28E-15;
mr1335 (All); LR P-value: 1.18E-12; mr1514 (All); LR P-value: 4.89E-08; mr1680 (All); LR P-value: 4.02E-07; mr1842 (All); LR P-value: 1.12E-17; mr1902 (All); LR P-value: 1.80E-11; mr1979 (All); LR P-value: 9.84E-08; mr1216_2 (All); LR P-value: 1.86E-11; mr1276_2 (All); LR P-value: 1.65E-19; mr1705_2 (All); LR P-value: 4.32E-09; mr1842_2 (All); LR P-value: 2.65E-16 |
LOC_Os03g55990.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g55990.3 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g55990.2 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os03g55990.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55990.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55990.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.036; most accessible tissue: Zhenshan97 flower, score: 97.697 |
| vg0331869518 (J) | chr03 | 31869518 | CCGG | C | 99.80% | 0.00% | CCGG -> C | NA |
LOC_Os03g55990.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55990.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55990.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55980.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.971; most accessible tissue: Zhenshan97 flower, score: 97.875 |
| vg0331869585 (J) | chr03 | 31869585 | G | C | 99.30% | 0.42% | G -> C | NA |
LOC_Os03g55990.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55990.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55990.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55980.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.676; most accessible tissue: Zhenshan97 flower, score: 96.466 |
| vg0331869698 (J) | chr03 | 31869698 | T | Unkown | 92.20% | 4.68% | T -> G | NA |
LOC_Os03g55990.3 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g55990.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: G| missense_variant MODERATE(snpEff) LOC_Os03g55990.3 Alt: G| missense_variant MODERATE(snpEff) LOC_Os03g55990.2 Alt: G| missense_variant MODERATE(snpEff) LOC_Os03g55980.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.445; most accessible tissue: Zhenshan97 flower, score: 96.028 |
| vg0331869712 (J) | chr03 | 31869712 | G | Unkown | 91.90% | 5.14% | G -> A | NA |
LOC_Os03g55990.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g55990.3 Alt: A| synonymous_variant LOW(snpEff) LOC_Os03g55990.2 Alt: A| synonymous_variant LOW(snpEff) LOC_Os03g55980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g55990.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.025; most accessible tissue: Zhenshan97 flower, score: 95.679 |
| vg0331869768 (J) | chr03 | 31869768 | A | Unkown | 93.20% | 3.91% | A -> T | NA |
LOC_Os03g55990.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g55990.3 Alt: T| missense_variant MODERATE(snpEff) LOC_Os03g55990.2 Alt: T| missense_variant MODERATE(snpEff) LOC_Os03g55980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g55990.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.475; most accessible tissue: Zhenshan97 flower, score: 93.754 |
| vg0331869941 (J) | chr03 | 31869941 | T | C | 56.20% | 0.04% | C -> T | NA |
LOC_Os03g55990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g55990.3 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os03g55990.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os03g55990.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 80.069; most accessible tissue: Zhenshan97 flower, score: 91.056 |
| vg0331869945 (J) | chr03 | 31869945 | C | T | 95.00% | 0.00% | C -> T | NA |
LOC_Os03g55990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g55990.3 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os03g55990.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 80.037; most accessible tissue: Zhenshan97 flower, score: 91.021 |
| vg0331869952 (J) | chr03 | 31869952 | G | T | 99.60% | 0.30% | G -> T | NA |
LOC_Os03g55990.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g55990.3 Alt: T| missense_variant MODERATE(snpEff) LOC_Os03g55990.2 Alt: T| missense_variant MODERATE(snpEff) LOC_Os03g55980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.063; most accessible tissue: Zhenshan97 flower, score: 90.696 |
| vg0331869964 (J) | chr03 | 31869964 | T | C | 97.60% | 1.88% | T -> C | NA |
LOC_Os03g55990.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g55990.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g55990.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 80.044; most accessible tissue: Zhenshan97 flower, score: 90.733 |
| vg0331870013 (J) | chr03 | 31870013 | GGTT | TGTT | 97.50% | 1.48% | GGTT -> TGTT,G | NA |
LOC_Os03g55990.2 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g55990.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: G| inframe_deletion MODERATE(snpEff) LOC_Os03g55990.2 Alt: G| inframe_deletion MODERATE(snpEff) LOC_Os03g55990.3 Alt: G| splice_region_variant&intron_variant LOW(snpEff) LOC_Os03g56000.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g55980.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g55990.1 Alt: TGTT| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os03g55990.2 Alt: TGTT| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 79.937; most accessible tissue: Zhenshan97 flower, score: 90.915 |
| vg0331870033 (J) | chr03 | 31870033 | T | C | 98.90% | 0.63% | T -> C | NA |
LOC_Os03g55990.3 Alt: C| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g55990.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g55990.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g55990.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 79.010; most accessible tissue: Zhenshan97 flower, score: 89.728 |
| vg0331870072 (J) | chr03 | 31870072 | T | A | 85.20% | 4.61% | T -> A | NA |
LOC_Os03g55990.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g55990.3 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os03g55990.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os03g55990.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 75.922; most accessible tissue: Zhenshan97 flower, score: 88.518 |
| vg0331870098 (J) | chr03 | 31870098 | GC | G | 99.20% | 0.00% | GC -> G | NA |
LOC_Os03g55990.1 Alt: G| frameshift_variant HIGH(snpEff)
LOC_Os03g55990.3 Alt: G| frameshift_variant HIGH(snpEff) LOC_Os03g55990.2 Alt: G| frameshift_variant HIGH(snpEff) LOC_Os03g56000.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.274; most accessible tissue: Zhenshan97 flower, score: 89.455 |
| vg0331870130 (J) | chr03 | 31870130 | G | A | 62.00% | 5.21% | A -> G | NA |
LOC_Os03g55990.3 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g55990.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os03g55990.3 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os03g55990.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 75.926; most accessible tissue: Zhenshan97 flower, score: 90.660 |
| vg0331870174 (J) | chr03 | 31870174 | C | G | 94.90% | 0.00% | C -> G | NA |
LOC_Os03g55990.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g55990.3 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os03g55990.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 76.716; most accessible tissue: Zhenshan97 flower, score: 91.419 |
| vg0331870381 (J) | chr03 | 31870381 | C | G | 99.30% | 0.36% | C -> G | NA |
LOC_Os03g55990.3 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g55990.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g55990.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g55990.3 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 65.114; most accessible tissue: Zhenshan97 flower, score: 89.944 |
| vg0331870487 (J) | chr03 | 31870487 | G | A | 98.80% | 0.78% | G -> A | NA |
LOC_Os03g55990.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55990.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56000.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55990.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 56.783; most accessible tissue: Zhenshan97 flower, score: 86.118 |
| vg0331870496 (J) | chr03 | 31870496 | G | A | 98.70% | 0.00% | G -> A | NA |
LOC_Os03g55990.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g55990.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g56000.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g55980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g55990.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 56.138; most accessible tissue: Zhenshan97 flower, score: 85.963 |
| vg0331870528 (J) | chr03 | 31870528 | T | A | 99.40% | 0.00% | T -> A | NA |
LOC_Os03g55990.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g55990.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56000.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55990.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.672; most accessible tissue: Zhenshan97 flower, score: 85.053 |
| vg0331870562 (J) | chr03 | 31870562 | T | G | 61.80% | 0.00% | G -> T |
LOC_Os03g55990.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56000.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55990.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g55990.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 52.595; most accessible tissue: Zhenshan97 flower, score: 83.061 |
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