37 variations found. LOC_Os01g22980 (OsSCP3 - Putative Serine Carboxypeptidase homologue; expressed), ranging from 12,914,947 bp to 12,919,210 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0112915067 (J) | chr01 | 12915067 | T | C | 97.40% | 0.00% | T -> C | NA |
LOC_Os01g22954.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 66.989; most accessible tissue: Minghui63 flag leaf, score: 90.086 |
| vg0112915145 (J) | chr01 | 12915145 | A | T | 99.80% | 0.00% | A -> T | NA |
LOC_Os01g22954.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g22980.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os01g22980.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) The average chromatin accessibility score: 60.975; most accessible tissue: Minghui63 flag leaf, score: 87.461 |
| vg0112915255 (J) | chr01 | 12915255 | C | T | 87.80% | 0.02% | C -> T |
mr1004 (All); LR P-value: 1.77E-06;
mr1095 (All); LR P-value: 8.50E-23; mr1098 (All); LR P-value: 3.72E-29; mr1099 (All); LR P-value: 1.26E-27; mr1101 (All); LR P-value: 1.22E-26; mr1180 (All); LR P-value: 6.83E-12; mr1210 (All); LR P-value: 2.11E-21; mr1305 (All); LR P-value: 1.82E-23; mr1515 (All); LR P-value: 6.55E-19; mr1586 (All); LR P-value: 3.23E-26; mr1589 (All); LR P-value: 2.76E-21; mr1858 (All); LR P-value: 2.06E-25; mr1859 (All); LR P-value: 1.87E-25; mr1868 (All); LR P-value: 6.84E-25; mr1095_2 (All); LR P-value: 1.20E-20; mr1098_2 (All); LR P-value: 1.94E-29; mr1099_2 (All); LR P-value: 6.44E-24; mr1305_2 (All); LR P-value: 1.96E-21; mr1792_2 (All); LR P-value: 7.01E-07; mr1803_2 (All); LR P-value: 1.44E-14; mr1815_2 (All); LR P-value: 3.70E-06; mr1874_2 (All); LR P-value: 1.02E-17; mr1929_2 (All); LR P-value: 3.84E-06 |
LOC_Os01g22954.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22980.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 55.610; most accessible tissue: Zhenshan97 young leaf, score: 78.044 |
| vg0112915297 (J) | chr01 | 12915297 | C | G | 90.60% | 0.00% | C -> G | NA |
LOC_Os01g22954.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22980.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 52.318; most accessible tissue: Callus, score: 76.955 |
| vg0112915485 (J) | chr01 | 12915485 | A | G | 67.90% | 0.00% | G -> A | NA |
LOC_Os01g22980.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22980.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22954.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.674; most accessible tissue: Callus, score: 79.829 |
| vg0112915535 (J) | chr01 | 12915535 | A | G | 97.50% | 0.00% | A -> G | NA |
LOC_Os01g22980.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22980.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22954.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.491; most accessible tissue: Minghui63 flag leaf, score: 82.750 |
| vg0112915801 (J) | chr01 | 12915801 | G | T | 98.60% | 0.00% | G -> T | NA |
LOC_Os01g22954.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22980.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.967; most accessible tissue: Minghui63 flag leaf, score: 84.608 |
| vg0112915805 (J) | chr01 | 12915805 | A | G | 99.60% | 0.00% | A -> G | NA |
LOC_Os01g22954.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g22980.1 Alt: G| intron_variant MODIFIER(snpEff) LOC_Os01g22980.2 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.063; most accessible tissue: Minghui63 flag leaf, score: 85.500 |
| vg0112915913 (J) | chr01 | 12915913 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os01g22980.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g22980.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 69.790; most accessible tissue: Zhenshan97 panicle, score: 81.135 |
| vg0112916401 (J) | chr01 | 12916401 | A | G | 67.90% | 0.00% | G -> A | NA |
LOC_Os01g22980.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g22980.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 59.423; most accessible tissue: Zhenshan97 young leaf, score: 75.751 |
| vg0112916471 (J) | chr01 | 12916471 | G | T | 66.40% | 0.00% | T -> G |
mr1134 (All); LR P-value: 2.56E-83;
mr1383 (All); LR P-value: 2.07E-24; mr1480 (All); LR P-value: 1.61E-39; mr1711 (All); LR P-value: 6.56E-66; mr1932 (All); LR P-value: 7.15E-36; mr1935 (All); LR P-value: 4.44E-52; mr1968 (All); LR P-value: 2.43E-16; mr1134_2 (All); LR P-value: 2.56E-97; mr1146_2 (All); LR P-value: 8.06E-18; mr1150_2 (All); LR P-value: 6.31E-32; mr1168_2 (All); LR P-value: 1.97E-21; mr1711_2 (All); LR P-value: 1.86E-89; mr1712_2 (All); LR P-value: 1.88E-18; mr1730_2 (All); LR P-value: 1.75E-16; mr1817_2 (All); LR P-value: 5.61E-18; mr1836_2 (All); LR P-value: 9.33E-17; mr1866_2 (All); LR P-value: 2.81E-15; mr1893_2 (All); LR P-value: 2.51E-11; mr1986_2 (All); LR P-value: 6.60E-11 |
LOC_Os01g22954.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22990.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22990.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.001; most accessible tissue: Callus, score: 87.111 |
| vg0112916699 (J) | chr01 | 12916699 | GT | G | 99.70% | 0.00% | GT -> G | NA |
LOC_Os01g22954.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22990.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22990.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.700; most accessible tissue: Callus, score: 87.617 |
| vg0112916720 (J) | chr01 | 12916720 | C | T | 62.40% | 0.53% | C -> T | NA |
LOC_Os01g22954.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22990.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22990.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 67.793; most accessible tissue: Callus, score: 87.617 |
| vg0112917092 (J) | chr01 | 12917092 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os01g22954.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22990.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22990.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.637; most accessible tissue: Minghui63 flag leaf, score: 69.681 |
| vg0112917258 (J) | chr01 | 12917258 | A | G | 98.80% | 0.00% | A -> G | NA |
LOC_Os01g22954.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22990.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22990.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.674; most accessible tissue: Callus, score: 80.533 |
| vg0112917528 (J) | chr01 | 12917528 | A | G | 74.10% | 0.19% | A -> G |
LOC_Os01g22954.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22990.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22990.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.312; most accessible tissue: Zhenshan97 root, score: 90.023 |
|
| vg0112917586 (J) | chr01 | 12917586 | G | C | 99.00% | 0.00% | G -> C | NA |
LOC_Os01g22954.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22990.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.808; most accessible tissue: Zhenshan97 root, score: 91.763 |
| vg0112917605 (J) | chr01 | 12917605 | G | T | 99.20% | 0.00% | G -> T | NA |
LOC_Os01g22954.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g22990.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g22990.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g22980.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os01g22980.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.039; most accessible tissue: Zhenshan97 root, score: 92.693 |
| vg0112917710 (J) | chr01 | 12917710 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os01g22954.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g22990.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g22990.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g22980.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os01g22980.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.136; most accessible tissue: Zhenshan97 root, score: 94.531 |
| vg0112917801 (J) | chr01 | 12917801 | T | C | 96.60% | 0.00% | T -> C |
LOC_Os01g22954.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22990.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.065; most accessible tissue: Zhenshan97 root, score: 94.234 |
|
| vg0112917856 (J) | chr01 | 12917856 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os01g22954.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g22990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g22990.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g22980.1 Alt: C| intron_variant MODIFIER(snpEff) LOC_Os01g22980.2 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.465; most accessible tissue: Zhenshan97 root, score: 93.917 |
| vg0112917859 (J) | chr01 | 12917859 | G | T | 62.40% | 0.53% | G -> T | NA |
LOC_Os01g22954.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22990.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22990.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 80.020; most accessible tissue: Zhenshan97 root, score: 93.917 |
| vg0112917980 (J) | chr01 | 12917980 | T | C | 98.20% | 0.00% | T -> C | NA |
LOC_Os01g22954.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22990.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.531; most accessible tissue: Callus, score: 92.651 |
| vg0112917992 (J) | chr01 | 12917992 | G | T | 66.40% | 0.00% | T -> G |
mr1134 (All); LR P-value: 2.56E-83;
mr1383 (All); LR P-value: 2.07E-24; mr1480 (All); LR P-value: 1.61E-39; mr1711 (All); LR P-value: 6.56E-66; mr1932 (All); LR P-value: 7.15E-36; mr1935 (All); LR P-value: 4.44E-52; mr1968 (All); LR P-value: 2.43E-16; mr1134_2 (All); LR P-value: 2.56E-97; mr1146_2 (All); LR P-value: 8.06E-18; mr1150_2 (All); LR P-value: 6.31E-32; mr1168_2 (All); LR P-value: 1.97E-21; mr1711_2 (All); LR P-value: 1.86E-89; mr1712_2 (All); LR P-value: 1.88E-18; mr1730_2 (All); LR P-value: 1.75E-16; mr1817_2 (All); LR P-value: 5.61E-18; mr1836_2 (All); LR P-value: 9.33E-17; mr1866_2 (All); LR P-value: 2.81E-15; mr1893_2 (All); LR P-value: 2.51E-11; mr1986_2 (All); LR P-value: 6.60E-11 |
LOC_Os01g22954.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g22990.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22990.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g22980.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.174; most accessible tissue: Callus, score: 92.651 |
| vg0112918170 (J) | chr01 | 12918170 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os01g22954.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g22990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g22990.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g22980.1 Alt: C| intron_variant MODIFIER(snpEff) LOC_Os01g22980.2 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 73.834; most accessible tissue: Minghui63 flag leaf, score: 87.461 |
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