22 variations found. LOC_Os02g10420 (expressed protein), ranging from 5,477,109 bp to 5,478,166 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0205477420 (J) | chr02 | 5477420 | T | A | 75.50% | 9.84% | T -> A | NA |
LOC_Os02g10420.1 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g10420.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.758; most accessible tissue: Minghui63 flower, score: 92.813 |
| vg0205477422 (J) | chr02 | 5477422 | CTTTGAG AT | C | 99.80% | 0.00% | CTTTGAGAT -> C | NA |
LOC_Os02g10420.1 Alt: C| splice_acceptor_variant&splice_region_variant&intron_variant HIGH(snpEff)
LOC_Os02g10400.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10410.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g10430.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.777; most accessible tissue: Minghui63 flower, score: 92.842 |
| vg0205477423 (J) | chr02 | 5477423 | T | TGCTCCG CCGCCGC CGCCGCC ATCGCCG CCGGTGA CCGGCGC CCGG | 87.30% | 0.00% | T -> TGCTCCGCCG CCGCCGCCGC CATCGCCGCC GGTGACCGGC GCCCGGTTGG TTGGTTAG,T GCTCCGCCGC CGCCGCCGCC ATCGCCGCCG GTGACCGGCG CCCGGTTGGT TGG,TGCTCC GCCGCCGCCG CCGCCATCGC CGCCGGTGAC CGGCGCCCGG TTGG,TGC,T GCTCCGCCGC CGCCGCCGCC ATCGCCGCCG G,TGCTCCGC CGCCGCCGCC GCCATCGCCG CCGGTGACCG GCGCCCGG | NA |
LOC_Os02g10420.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGG| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g10400.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGGTTGGTTAG| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGGTTGGTTAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGGTTGGTTAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGGTTGGTTAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGGTTGGTTAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGGTTGG| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGGTTGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGGTTGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGGTTGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGGTTGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGG| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGGTGACCGGCGCCCGGTTGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGG| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TGCTCCGCCGCCGCCGCCGCCATCGCCGCCGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TGC| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: TGC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TGC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TGC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TGC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.777; most accessible tissue: Minghui63 flower, score: 92.842 |
| vg0205477424 (J) | chr02 | 5477424 | T | TCCGCCG CCGCCGC CGCCATC GCCGCCG G | 80.00% | 10.16% | T -> TCCGCCGCCG CCGCCGCCAT CGCCGCCGG | NA |
LOC_Os02g10420.1 Alt: TCCGCCGCCGCCGCCGCCATCGCCGCCGG| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g10400.1 Alt: TCCGCCGCCGCCGCCGCCATCGCCGCCGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TCCGCCGCCGCCGCCGCCATCGCCGCCGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TCCGCCGCCGCCGCCGCCATCGCCGCCGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TCCGCCGCCGCCGCCGCCATCGCCGCCGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.762; most accessible tissue: Minghui63 flower, score: 92.842 |
| vg0205477425 (J) | chr02 | 5477425 | T | C | 79.80% | 10.14% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g10420.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.122; most accessible tissue: Minghui63 flower, score: 92.842 |
| vg0205477426 (J) | chr02 | 5477426 | G | T | 76.50% | 7.85% | G -> T | NA |
LOC_Os02g10420.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g10400.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 88.000; most accessible tissue: Minghui63 flower, score: 92.813 |
| vg0205477433 (J) | chr02 | 5477433 | A | C | 84.10% | 6.03% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g10400.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.936; most accessible tissue: Minghui63 flower, score: 92.813 |
| vg0205477465 (J) | chr02 | 5477465 | G | A | 78.00% | 0.02% | G -> A |
mr1032 (Ind_All); LR P-value: 2.07E-06;
mr1170 (Ind_All); LR P-value: 4.97E-08; mr1478 (Ind_All); LR P-value: 7.24E-06; mr1593 (All); LR P-value: 2.59E-08; mr1696 (All); LR P-value: 7.32E-12; mr1696 (Jap_All); LR P-value: 3.17E-07; mr1158_2 (All); LR P-value: 4.34E-06; mr1170_2 (Ind_All); LR P-value: 3.91E-06; mr1593_2 (All); LR P-value: 6.46E-12; mr1696_2 (Jap_All); LR P-value: 1.11E-08 |
LOC_Os02g10400.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 87.637; most accessible tissue: Minghui63 flower, score: 92.871 |
| vg0205477511 (J) | chr02 | 5477511 | C | A | 97.20% | 0.00% | C -> A | NA |
LOC_Os02g10400.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.780; most accessible tissue: Minghui63 flower, score: 92.249 |
| vg0205477564 (J) | chr02 | 5477564 | TGAAGAA GAAGAAG AAGAAGA AGAA | T | 65.60% | 0.00% | TGAAGAAGAA GAAGAAGAAG AAGAA -> T,TGAAGAAG AAGAAGAAGA AGAAGAAGAA ,TGAAGAAGA AGAAGAAGAA GAAGAAGAAG AA,TGAAGAA GAAGAAGAAG AA,TGAAGAA GAAGAAGAAG AAGAA,TGAA GAAGAAGAAG AA | NA |
LOC_Os02g10400.1 Alt: TGAAGAAGAAGAAGAAGAAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: TGAAGAAGAAGAAGAAGAAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TGAAGAAGAAGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TGAAGAAGAAGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TGAAGAAGAAGAAGAAGAAGAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: TGAAGAAGAAGAAGAAGAAGAAGAAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TGAAGAAGAAGAAGAAGAAGAAGAAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TGAAGAAGAAGAAGAAGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TGAAGAAGAAGAAGAAGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TGAAGAAGAAGAAGAAGAAGAAGAAGAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: TGAAGAAGAAGAAGAAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TGAAGAAGAAGAAGAAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TGAAGAAGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TGAAGAAGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TGAAGAAGAAGAAGAAGAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: TGAAGAAGAAGAAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TGAAGAAGAAGAAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TGAAGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TGAAGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TGAAGAAGAAGAAGAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: TGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.651; most accessible tissue: Minghui63 flower, score: 90.249 |
| vg0205477583 (J) | chr02 | 5477583 | GAAGAAG AAGAAGA AGAAGAA GAAGAAG AAGAAGA AGAAAGG CTTCA | G | 86.20% | 1.90% | GAAGAAGAAG AAGAAGAAGA AGAAGAAGAA GAAGAAGAAA GGCTTCA -> G | NA |
LOC_Os02g10400.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 73.583; most accessible tissue: Minghui63 flower, score: 89.262 |
| vg0205477584 (J) | chr02 | 5477584 | A | AGCT | 89.00% | 2.26% | A -> AGCT | NA |
LOC_Os02g10400.1 Alt: AGCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: AGCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: AGCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: AGCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: AGCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 73.583; most accessible tissue: Minghui63 flower, score: 89.262 |
| vg0205477735 (J) | chr02 | 5477735 | A | AT | 60.60% | 0.00% | A -> AT | NA |
LOC_Os02g10400.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.793; most accessible tissue: Minghui63 flower, score: 85.573 |
| vg0205477743 (J) | chr02 | 5477743 | TAA | TAAA | 97.00% | 0.00% | TAA -> TAAA,AAA,T | NA |
LOC_Os02g10400.1 Alt: AAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: AAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: AAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: AAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: AAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: AAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: TAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: TAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: TAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 52.295; most accessible tissue: Minghui63 flower, score: 86.369 |
| vg0205477744 (J) | chr02 | 5477744 | A | T | 83.20% | 2.56% | A -> T |
LOC_Os02g10400.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 54.171; most accessible tissue: Minghui63 flower, score: 87.009 |
|
| vg0205477776 (J) | chr02 | 5477776 | C | T | 60.50% | 31.19% | C -> T | NA |
LOC_Os02g10400.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 57.622; most accessible tissue: Minghui63 flower, score: 88.423 |
| vg0205477778 (J) | chr02 | 5477778 | TA | T | 57.70% | 0.00% | TA -> T,TAA | NA |
LOC_Os02g10400.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: TAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.552; most accessible tissue: Minghui63 flower, score: 88.359 |
| vg0205477779 (J) | chr02 | 5477779 | A | T | 91.00% | 1.88% | A -> T |
LOC_Os02g10400.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 57.558; most accessible tissue: Minghui63 flower, score: 88.423 |
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| vg0205478035 (J) | chr02 | 5478035 | AG | A | 94.00% | 0.99% | AG -> A | NA |
LOC_Os02g10400.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 61.692; most accessible tissue: Zhenshan97 flower, score: 91.158 |
| vg0205478037 (J) | chr02 | 5478037 | G | GA | 82.40% | 0.00% | G -> GA,A,GAA | NA |
LOC_Os02g10400.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10400.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10410.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.407; most accessible tissue: Zhenshan97 flower, score: 91.322 |
| vg0205478113 (J) | chr02 | 5478113 | T | A | 96.90% | 0.00% | T -> A | NA |
LOC_Os02g10400.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g10410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10440.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10430.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g10420.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.255; most accessible tissue: Zhenshan97 flower, score: 91.021 |
| STR0205477779 (J) | chr02 | 5477779 | AA | AAA | 49.60% | 0.00% | AA -> A,AAA | NA |
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