29 variations found. LOC_Os10g10060 (expressed protein), ranging from 5,470,931 bp to 5,471,475 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1005470944 (J) | chr10 | 5470944 | G | C | 86.50% | 10.85% | G -> C |
LOC_Os10g10060.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.218; most accessible tissue: Zhenshan97 flower, score: 93.614 |
|
| vg1005470947 (J) | chr10 | 5470947 | T | C | 82.10% | 15.09% | T -> C | NA |
LOC_Os10g10060.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.231; most accessible tissue: Zhenshan97 flower, score: 93.655 |
| vg1005470955 (J) | chr10 | 5470955 | A | T | 82.10% | 15.09% | A -> T | NA |
LOC_Os10g10060.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 80.609; most accessible tissue: Zhenshan97 flower, score: 93.655 |
| vg1005471015 (J) | chr10 | 5471015 | G | T | 82.50% | 14.96% | G -> T | NA |
LOC_Os10g10060.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.766; most accessible tissue: Zhenshan97 flower, score: 94.410 |
| vg1005471023 (J) | chr10 | 5471023 | A | AGC | 84.10% | 13.31% | A -> AGC,AGCCAG ATGGGCCAGA CTATGGGCCA CTTTATTCG, AGCCAGATGG GCCAGACTAT GGGCCACCTT ATTCG,AGCC AGATGGGCCA GACTATGGGC CAC,AGCCAG ATGGGCCAGA CTATGGGC,A GCCAGATGGG C | NA |
LOC_Os10g10060.1 Alt: AGC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os10g10060.1 Alt: AGCCAGATGGGCCAGACTATGGGCCACTTTATTCG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os10g10060.1 Alt: AGCCAGATGGGCCAGACTATGGGC| frameshift_variant&stop_gained HIGH(snpEff) LOC_Os10g10040.1 Alt: AGCCAGATGGGCCAGACTATGGGC| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g10050.1 Alt: AGCCAGATGGGCCAGACTATGGGC| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g10060.1 Alt: AGCCAGATGGGC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os10g10060.1 Alt: AGCCAGATGGGCCAGACTATGGGCCACCTTATTCG| frameshift_variant HIGH(snpEff) LOC_Os10g10040.1 Alt: AGCCAGATGGGCCAGACTATGGGCCACCTTATTCG| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g10050.1 Alt: AGCCAGATGGGCCAGACTATGGGCCACCTTATTCG| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g10060.1 Alt: AGCCAGATGGGCCAGACTATGGGCCAC| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 83.000; most accessible tissue: Zhenshan97 flower, score: 94.586 |
| vg1005471025 (J) | chr10 | 5471025 | A | AGATGGG CCAGACT ATGGGCC ACCTTAT TCGCATT CCTACTA ACTGAAA CG | 83.60% | 13.01% | A -> AGATGGGCCA GACTATGGGC CACTTTATTC GCATTCCTAC TAACTGAAAC G,AGATGGGC CAGACTATGG GCCACCTTAT TCGCATTCCT ACTAACTGAA ACG,AG,AGA TGGGCCAGAT GAGCCAGATG AGCCAGATGG GCCACCTTAT TCGCATTCCT ACTAACTGAA ACG,AGATGG GCCAGACT,A GATGGGCCAG ACTATGGGCC ACCTTATTCG CATTCCTACT | NA |
LOC_Os10g10060.1 Alt: AGATGGGCCAGACT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os10g10060.1 Alt: AGATGGGCCAGACTATGGGCCACTTTATTCGCATTCCTACTAACTGAAACG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os10g10060.1 Alt: AG| frameshift_variant HIGH(snpEff) LOC_Os10g10040.1 Alt: AG| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g10050.1 Alt: AG| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g10060.1 Alt: AGATGGGCCAGACTATGGGCCACCTTATTCGCATTCCTACTAACTGAAACG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os10g10060.1 Alt: AGATGGGCCAGACTATGGGCCACCTTATTCGCATTCCTACT| frameshift_variant HIGH(snpEff) LOC_Os10g10040.1 Alt: AGATGGGCCAGACTATGGGCCACCTTATTCGCATTCCTACT| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g10060.1 Alt: AGATGGGCCAGATGAGCCAGATGAGCCAGATGGGCCACCTTATTCGCATTCCTACTAACTGAAACG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 83.233; most accessible tissue: Zhenshan97 flower, score: 94.601 |
| vg1005471037 (J) | chr10 | 5471037 | G | A | 82.10% | 15.02% | G -> A | NA |
LOC_Os10g10060.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.688; most accessible tissue: Zhenshan97 flower, score: 94.724 |
| vg1005471043 (J) | chr10 | 5471043 | C | CAAA | 87.60% | 11.62% | C -> CAAA | NA |
LOC_Os10g10060.1 Alt: CAAA| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.734; most accessible tissue: Zhenshan97 flower, score: 94.855 |
| vg1005471086 (J) | chr10 | 5471086 | T | C | 82.00% | 15.21% | T -> C | NA |
LOC_Os10g10060.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.096; most accessible tissue: Zhenshan97 flower, score: 95.918 |
| vg1005471101 (J) | chr10 | 5471101 | T | C | 78.80% | 15.57% | T -> C | NA |
LOC_Os10g10060.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.101; most accessible tissue: Zhenshan97 flower, score: 95.998 |
| vg1005471152 (J) | chr10 | 5471152 | A | T | 85.40% | 11.43% | A -> T | NA |
LOC_Os10g10060.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.374; most accessible tissue: Zhenshan97 flower, score: 96.440 |
| vg1005471156 (J) | chr10 | 5471156 | G | GTGTGGA GATTATG GGTACCC | 86.90% | 11.40% | G -> GTGTGGAGAT TATGGGTACC CCATACC,GT GTGGAGATTA TGGGTACCC, GTGTGGAGAT TATGGGTACC CCATA,GTGT GGAGATTATG GGTACCCCAT ACCCACA,GT GTGGAGATTA TGGGTACCCC ATACCCA,GT GTGGAGATTA TGGGTA | NA |
LOC_Os10g10060.1 Alt: GTGTGGAGATTATGGGTA| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os10g10060.1 Alt: GTGTGGAGATTATGGGTACCCCATACCCACA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os10g10060.1 Alt: GTGTGGAGATTATGGGTACCCCATACC| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os10g10060.1 Alt: GTGTGGAGATTATGGGTACCCCATA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os10g10060.1 Alt: GTGTGGAGATTATGGGTACCC| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os10g10060.1 Alt: GTGTGGAGATTATGGGTACCCCATACCCA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 85.261; most accessible tissue: Zhenshan97 flower, score: 96.424 |
| vg1005471157 (J) | chr10 | 5471157 | C | G | 88.00% | 11.40% | C -> G,T | NA |
LOC_Os10g10060.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: T| missense_variant MODERATE(snpEff) LOC_Os10g10040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g10050.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.261; most accessible tissue: Zhenshan97 flower, score: 96.424 |
| vg1005471160 (J) | chr10 | 5471160 | C | G | 88.00% | 11.34% | C -> G | NA |
LOC_Os10g10060.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.425; most accessible tissue: Zhenshan97 flower, score: 96.499 |
| vg1005471162 (J) | chr10 | 5471162 | T | G | 88.00% | 11.34% | T -> G | NA |
LOC_Os10g10060.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.408; most accessible tissue: Zhenshan97 flower, score: 96.491 |
| vg1005471181 (J) | chr10 | 5471181 | CTTAA | C | 82.60% | 14.64% | CTTAA -> C | NA |
LOC_Os10g10060.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.475; most accessible tissue: Zhenshan97 flower, score: 96.732 |
| vg1005471194 (J) | chr10 | 5471194 | ATCACG | A | 84.50% | 14.18% | ATCACG -> A | NA |
LOC_Os10g10060.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.005; most accessible tissue: Zhenshan97 flower, score: 96.264 |
| vg1005471198 (J) | chr10 | 5471198 | CGT | C | 84.70% | 12.63% | CGT -> C | NA |
LOC_Os10g10060.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.964; most accessible tissue: Zhenshan97 flower, score: 96.264 |
| vg1005471201 (J) | chr10 | 5471201 | CACG | C | 84.70% | 12.97% | CACG -> C | NA |
LOC_Os10g10060.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.492; most accessible tissue: Zhenshan97 flower, score: 96.199 |
| vg1005471212 (J) | chr10 | 5471212 | G | A | 82.40% | 14.88% | G -> A | NA |
LOC_Os10g10060.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.713; most accessible tissue: Zhenshan97 flower, score: 96.209 |
| vg1005471213 (J) | chr10 | 5471213 | T | C | 79.40% | 15.38% | T -> C | NA |
LOC_Os10g10060.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g10060.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.713; most accessible tissue: Zhenshan97 flower, score: 96.209 |
| vg1005471243 (J) | chr10 | 5471243 | G | A | 66.30% | 12.93% | A -> G |
LOC_Os10g10060.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.964; most accessible tissue: Zhenshan97 flower, score: 94.754 |
|
| vg1005471291 (J) | chr10 | 5471291 | G | A | 82.00% | 15.26% | G -> A | NA |
LOC_Os10g10060.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g10060.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.646; most accessible tissue: Zhenshan97 flower, score: 94.663 |
| vg1005471328 (J) | chr10 | 5471328 | A | G | 82.20% | 14.75% | A -> G | NA |
LOC_Os10g10060.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os10g10040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10050.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.788; most accessible tissue: Zhenshan97 flower, score: 93.594 |
| vg1005471343 (J) | chr10 | 5471343 | G | A | 82.40% | 14.85% | G -> A | NA |
LOC_Os10g10040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g10050.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10060.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.996; most accessible tissue: Zhenshan97 flower, score: 93.362 |
| vg1005471382 (J) | chr10 | 5471382 | T | TCAATAC AGAAG | 86.20% | 12.61% | T -> TCAATACAGA AG,TCAA,TC AATACAGAAG TTACAATAAA A,TCAATACA GAAGTTACAA | NA |
LOC_Os10g10040.1 Alt: TCAATACAGAAGTTACAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g10050.1 Alt: TCAATACAGAAGTTACAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10060.1 Alt: TCAATACAGAAGTTACAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10040.1 Alt: TCAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10050.1 Alt: TCAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10060.1 Alt: TCAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os10g10040.1 Alt: TCAATACAGAAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10050.1 Alt: TCAATACAGAAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10060.1 Alt: TCAATACAGAAG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10040.1 Alt: TCAATACAGAAGTTACAATAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10050.1 Alt: TCAATACAGAAGTTACAATAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10060.1 Alt: TCAATACAGAAGTTACAATAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.059; most accessible tissue: Zhenshan97 flower, score: 93.384 |
| vg1005471405 (J) | chr10 | 5471405 | G | T | 63.10% | 13.33% | G -> T |
mr1026 (Ind_All); LR P-value: 2.10E-11;
mr1114 (Ind_All); LR P-value: 1.04E-06; mr1116 (Ind_All); LR P-value: 6.02E-06; mr1118 (Ind_All); LMM P-value: 8.75E-07; LR P-value: 2.25E-13; mr1161 (Ind_All); LR P-value: 1.43E-10; mr1261 (Ind_All); LR P-value: 6.83E-06; mr1495 (Ind_All); LMM P-value: 7.61E-07; LR P-value: 3.52E-17; mr1113_2 (Ind_All); LR P-value: 2.37E-06; mr1114_2 (Ind_All); LR P-value: 3.73E-07; mr1118_2 (Ind_All); LMM P-value: 4.17E-08; LR P-value: 8.50E-16; mr1120_2 (Ind_All); LR P-value: 4.72E-07; mr1161_2 (Ind_All); LR P-value: 1.13E-11; mr1247_2 (Ind_All); LR P-value: 6.50E-06; mr1495_2 (Ind_All); LMM P-value: 1.02E-06; LR P-value: 5.74E-17 |
LOC_Os10g10040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g10050.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10060.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.095; most accessible tissue: Zhenshan97 flower, score: 93.189 |
| vg1005471422 (J) | chr10 | 5471422 | ATG | A | 63.10% | 13.12% | ATG -> A | NA |
LOC_Os10g10040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g10050.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10060.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.085; most accessible tissue: Zhenshan97 flower, score: 92.618 |
| vg1005471433 (J) | chr10 | 5471433 | T | C | 85.10% | 13.27% | T -> C |
LOC_Os10g10040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g10050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g10060.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.807; most accessible tissue: Zhenshan97 flower, score: 92.513 |