41 variations found. Os12g0115500/LOC_Os12g02340 (LTPL14 - Protease inhibitor%2Fseed storage%2FLTP family protein precursor; expressed), ranging from 760,918 bp to 762,534 bp (including 0 kb upstream and 0 kb downstream of the gene).
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os12g02340 | Os12g0115500 | OsLTP1.20 | non-specific lipid transfer protein 1.20, lipid transfer protein 1.20, type 1 non-specific lipid transfer protein 20 | _ | _ |
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1200760942 (J) | chr12 | 760942 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os12g02340.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)
LOC_Os12g02340.2 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os12g02340.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g02340.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g02350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.414; most accessible tissue: Zhenshan97 flower, score: 97.358 |
| vg1200760972 (J) | chr12 | 760972 | T | G | 99.80% | 0.00% | T -> G | NA |
LOC_Os12g02340.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os12g02340.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.553; most accessible tissue: Zhenshan97 flower, score: 96.982 |
| vg1200760985 (J) | chr12 | 760985 | CTCGATC ATCAGAT CA | C | 99.40% | 0.00% | CTCGATCATC AGATCA -> C | NA |
LOC_Os12g02340.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02340.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.976; most accessible tissue: Zhenshan97 flower, score: 97.138 |
| vg1200761104 (J) | chr12 | 761104 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os12g02340.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os12g02340.2 Alt: G| synonymous_variant LOW(snpEff) LOC_Os12g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.087; most accessible tissue: Zhenshan97 flower, score: 95.542 |
| vg1200761179 (J) | chr12 | 761179 | T | C | 51.00% | 0.00% | C -> T |
mr1278 (All); LR P-value: 8.18E-07;
mr1332 (All); LR P-value: 1.31E-08; mr1386 (All); LR P-value: 8.38E-12; mr1392 (All); LR P-value: 1.96E-07; mr1442 (All); LR P-value: 1.26E-09; mr1521 (All); LR P-value: 4.21E-12; mr1579 (All); LR P-value: 3.79E-12; mr1633 (All); LR P-value: 9.65E-07; mr1636 (All); LR P-value: 2.57E-13; mr1683 (All); LR P-value: 1.08E-13; mr1776 (All); LR P-value: 1.56E-08; mr1810 (All); LR P-value: 9.38E-08; mr1838 (All); LR P-value: 3.35E-20; mr1839 (All); LR P-value: 3.53E-21; mr1846 (All); LR P-value: 4.94E-11; mr1909 (All); LR P-value: 1.27E-15; mr1921 (All); LR P-value: 1.76E-11; mr1979 (All); LR P-value: 1.18E-06 |
LOC_Os12g02340.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g02340.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 74.202; most accessible tissue: Zhenshan97 flower, score: 95.601 |
| vg1200761332 (J) | chr12 | 761332 | G | A | 58.70% | 0.00% | A -> G |
mr1172 (All); LR P-value: 3.53E-11;
mr1184 (All); LR P-value: 6.37E-06; mr1278 (All); LR P-value: 8.67E-07; mr1315 (All); LR P-value: 1.24E-06; mr1336 (All); LR P-value: 5.51E-10; mr1386 (All); LR P-value: 7.86E-12; mr1392 (All); LR P-value: 1.96E-07; mr1442 (All); LR P-value: 3.20E-08; mr1461 (All); LR P-value: 6.83E-06; mr1579 (All); LR P-value: 2.17E-12; mr1633 (All); LR P-value: 2.22E-06; mr1636 (All); LR P-value: 6.86E-14; mr1659 (All); LR P-value: 1.80E-07; mr1683 (All); LR P-value: 5.27E-14; mr1767 (All); LR P-value: 3.99E-19; mr1776 (All); LR P-value: 1.46E-08; mr1810 (All); LR P-value: 4.56E-08; mr1838 (All); LR P-value: 1.62E-21; mr1839 (All); LR P-value: 3.82E-22; mr1886 (All); LR P-value: 1.44E-06; mr1909 (All); LR P-value: 8.43E-16; mr1921 (All); LR P-value: 5.93E-12 |
LOC_Os12g02340.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 69.871; most accessible tissue: Zhenshan97 flower, score: 95.554 |
| vg1200761409 (J) | chr12 | 761409 | TCC | TCCCC | 54.80% | 16.61% | TCC -> TCCCC,TCCC CCC,TCCCCC ,TCCC,TC,T | NA |
LOC_Os12g02350.1 Alt: TCCCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02340.1 Alt: TCCCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: TCCCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: TCCCCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: TCCCCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: TCCCCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: TCCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: TCCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: TCCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: TCCCCCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: TCCCCCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: TCCCCCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: TC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.783; most accessible tissue: Zhenshan97 flower, score: 94.158 |
| vg1200761416 (J) | chr12 | 761416 | CCT | CCCCACT | 80.10% | 6.77% | CCT -> CCCCACT,CC CCCACT,CCC ACT,TCT,C | NA |
LOC_Os12g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: CCCCACT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: CCCCACT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: CCCCACT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: CCCCCACT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: CCCCCACT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: CCCCCACT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: TCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: TCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: TCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: CCCACT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: CCCACT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: CCCACT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.173; most accessible tissue: Zhenshan97 flower, score: 94.071 |
| vg1200761417 (J) | chr12 | 761417 | CT | C | 84.50% | 7.81% | CT -> C | NA |
LOC_Os12g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 63.178; most accessible tissue: Zhenshan97 flower, score: 94.124 |
| vg1200761418 (J) | chr12 | 761418 | T | C | 54.80% | 14.94% | T -> C | NA |
LOC_Os12g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 61.669; most accessible tissue: Zhenshan97 flower, score: 93.870 |
| vg1200761420 (J) | chr12 | 761420 | T | C | 84.80% | 3.87% | T -> C,A | NA |
LOC_Os12g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.803; most accessible tissue: Zhenshan97 flower, score: 93.944 |
| vg1200761425 (J) | chr12 | 761425 | CTATA | CTA | 73.50% | 7.19% | CTATA -> CTA,C | NA |
LOC_Os12g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: CTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: CTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: CTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.355; most accessible tissue: Zhenshan97 flower, score: 93.870 |
| vg1200761427 (J) | chr12 | 761427 | A | C | 47.50% | 27.00% | A -> C | NA |
LOC_Os12g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 62.635; most accessible tissue: Zhenshan97 flower, score: 93.907 |
| vg1200761429 (J) | chr12 | 761429 | A | C | 50.10% | 27.66% | A -> C |
LOC_Os12g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 62.397; most accessible tissue: Zhenshan97 flower, score: 93.832 |
|
| vg1200761489 (J) | chr12 | 761489 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os12g02350.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g02370.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02340.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os12g02340.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 59.535; most accessible tissue: Zhenshan97 flower, score: 93.490 |
| vg1200761506 (J) | chr12 | 761506 | C | T | 92.90% | 0.00% | C -> T |
LOC_Os12g02350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.451; most accessible tissue: Zhenshan97 flower, score: 93.405 |
|
| vg1200761535 (J) | chr12 | 761535 | G | A | 91.30% | 0.00% | G -> A |
mr1038 (Ind_All); LR P-value: 3.23E-06;
mr1280 (All); LR P-value: 8.80E-06; mr1280 (Ind_All); LR P-value: 1.42E-06; mr1318 (Ind_All); LR P-value: 3.98E-06; mr1389 (All); LR P-value: 8.94E-08; mr1389 (Ind_All); LR P-value: 3.09E-07; mr1691 (Ind_All); LR P-value: 9.25E-08; mr1693 (Ind_All); LR P-value: 4.16E-07; mr1729 (All); LR P-value: 1.37E-06; mr1729 (Ind_All); LR P-value: 1.16E-06; mr1741 (Ind_All); LR P-value: 8.55E-06 |
LOC_Os12g02350.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.596; most accessible tissue: Zhenshan97 flower, score: 92.487 |
| vg1200761539 (J) | chr12 | 761539 | T | C | 93.00% | 0.00% | T -> C |
LOC_Os12g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.596; most accessible tissue: Zhenshan97 flower, score: 92.487 |
|
| vg1200761550 (J) | chr12 | 761550 | A | G | 92.20% | 0.00% | A -> G |
mr1053 (All); LR P-value: 8.83E-07;
mr1095 (All); LR P-value: 4.97E-24; mr1098 (All); LR P-value: 1.13E-32; mr1099 (All); LR P-value: 2.32E-29; mr1101 (All); LR P-value: 2.52E-27; mr1113 (All); LR P-value: 7.48E-15; mr1184 (All); LR P-value: 8.52E-06; mr1230 (All); LR P-value: 1.35E-06; mr1240 (All); LR P-value: 3.42E-16; mr1262 (All); LR P-value: 1.41E-06; mr1345 (All); LR P-value: 3.51E-06; mr1349 (All); LR P-value: 7.85E-06; mr1365 (All); LR P-value: 2.23E-06; mr1382 (All); LR P-value: 2.28E-06; mr1523 (All); LR P-value: 3.60E-06; mr1556 (All); LR P-value: 9.97E-07; mr1589 (All); LR P-value: 8.20E-23; mr1634 (All); LR P-value: 9.33E-06; mr1649 (All); LR P-value: 8.20E-12; mr1696 (All); LR P-value: 1.07E-10; mr1868 (All); LR P-value: 1.16E-25; mr1911 (All); LR P-value: 2.43E-19; mr1918 (All); LR P-value: 6.65E-13; mr1939 (All); LR P-value: 4.17E-09; mr1961 (All); LR P-value: 1.22E-19; mr1095_2 (All); LR P-value: 6.86E-24; mr1098_2 (All); LR P-value: 5.84E-33; mr1099_2 (All); LR P-value: 1.50E-26; mr1240_2 (All); LR P-value: 9.07E-18; mr1911_2 (All); LR P-value: 1.01E-17; mr1918_2 (All); LR P-value: 3.64E-13; mr1929_2 (All); LR P-value: 3.80E-06 |
LOC_Os12g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.662; most accessible tissue: Zhenshan97 flower, score: 91.701 |
| vg1200761620 (J) | chr12 | 761620 | C | T | 93.00% | 0.00% | C -> T |
LOC_Os12g02350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 39.973; most accessible tissue: Zhenshan97 flower, score: 86.416 |
|
| vg1200761646 (J) | chr12 | 761646 | CT | C | 58.30% | 0.00% | C -> CT,CTT,CTA | NA |
LOC_Os12g02350.1 Alt: CTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: CTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: CTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: CTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: CTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.2 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.2 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 32.038; most accessible tissue: Zhenshan97 flower, score: 78.677 |
| vg1200761652 (J) | chr12 | 761652 | T | TC | 99.30% | 0.00% | T -> TC | NA |
LOC_Os12g02350.1 Alt: TC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 32.535; most accessible tissue: Zhenshan97 flower, score: 78.500 |
| vg1200761684 (J) | chr12 | 761684 | G | A | 92.80% | 0.00% | G -> A |
LOC_Os12g02350.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 32.763; most accessible tissue: Zhenshan97 flower, score: 75.657 |
|
| vg1200761690 (J) | chr12 | 761690 | G | A | 97.00% | 0.00% | G -> A | NA |
LOC_Os12g02350.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 32.129; most accessible tissue: Zhenshan97 flower, score: 75.428 |
| vg1200761693 (J) | chr12 | 761693 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os12g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g02370.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02340.1 Alt: C| intron_variant MODIFIER(snpEff) LOC_Os12g02340.2 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 32.028; most accessible tissue: Zhenshan97 flower, score: 75.428 |
| vg1200761717 (J) | chr12 | 761717 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os12g02350.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g02370.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02340.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os12g02340.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 31.811; most accessible tissue: Zhenshan97 flower, score: 74.708 |
| vg1200761724 (J) | chr12 | 761724 | A | G | 92.90% | 0.00% | A -> G |
LOC_Os12g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 30.809; most accessible tissue: Zhenshan97 flower, score: 73.683 |
|
| vg1200761725 (J) | chr12 | 761725 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os12g02350.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 30.126; most accessible tissue: Zhenshan97 flower, score: 73.414 |
| vg1200761918 (J) | chr12 | 761918 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os12g02350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g02370.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.4 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02340.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os12g02340.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 29.281; most accessible tissue: Zhenshan97 flower, score: 73.946 |
| vg1200761930 (J) | chr12 | 761930 | T | C | 58.70% | 0.00% | C -> T |
mr1172 (All); LR P-value: 3.03E-11;
mr1184 (All); LR P-value: 4.41E-06; mr1278 (All); LR P-value: 7.80E-07; mr1315 (All); LR P-value: 9.33E-07; mr1336 (All); LR P-value: 7.49E-10; mr1386 (All); LR P-value: 6.09E-12; mr1392 (All); LR P-value: 1.69E-07; mr1442 (All); LR P-value: 2.11E-08; mr1461 (All); LR P-value: 4.45E-06; mr1545 (All); LR P-value: 8.93E-06; mr1579 (All); LR P-value: 1.67E-12; mr1633 (All); LR P-value: 1.52E-06; mr1636 (All); LR P-value: 3.04E-14; mr1659 (All); LR P-value: 1.32E-07; mr1683 (All); LR P-value: 2.15E-14; mr1767 (All); LR P-value: 3.71E-19; mr1776 (All); LR P-value: 8.32E-09; mr1810 (All); LR P-value: 3.33E-08; mr1838 (All); LR P-value: 1.06E-21; mr1839 (All); LR P-value: 2.81E-22; mr1886 (All); LR P-value: 9.56E-07; mr1909 (All); LR P-value: 5.57E-16; mr1921 (All); LR P-value: 4.47E-12 |
LOC_Os12g02350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 30.493; most accessible tissue: Zhenshan97 flower, score: 71.382 |
| vg1200761941 (J) | chr12 | 761941 | A | AT | 99.80% | 0.00% | A -> AT | NA |
LOC_Os12g02350.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g02370.2 Alt: AT| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.4 Alt: AT| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02340.1 Alt: AT| intron_variant MODIFIER(snpEff) LOC_Os12g02340.2 Alt: AT| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 30.932; most accessible tissue: Zhenshan97 flower, score: 71.992 |
| vg1200761994 (J) | chr12 | 761994 | TG | TGG | 99.90% | 0.00% | TG -> TGG,T | NA |
LOC_Os12g02350.1 Alt: TGG| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g02370.2 Alt: TGG| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.4 Alt: TGG| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02340.1 Alt: TGG| intron_variant MODIFIER(snpEff) LOC_Os12g02340.2 Alt: TGG| intron_variant MODIFIER(snpEff) LOC_Os12g02350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.4 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02340.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os12g02340.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 32.682; most accessible tissue: Zhenshan97 flower, score: 72.863 |
| vg1200762073 (J) | chr12 | 762073 | A | G | 58.70% | 0.00% | G -> A |
mr1172 (All); LR P-value: 7.47E-11;
mr1184 (All); LR P-value: 7.36E-06; mr1278 (All); LR P-value: 2.34E-06; mr1315 (All); LR P-value: 1.28E-06; mr1336 (All); LR P-value: 1.00E-09; mr1392 (All); LR P-value: 2.47E-07; mr1442 (All); LR P-value: 3.23E-08; mr1461 (All); LR P-value: 5.25E-06; mr1579 (All); LR P-value: 1.59E-12; mr1633 (All); LR P-value: 1.78E-06; mr1636 (All); LR P-value: 2.76E-14; mr1659 (All); LR P-value: 1.68E-07; mr1683 (All); LR P-value: 2.52E-14; mr1767 (All); LR P-value: 5.18E-19; mr1776 (All); LR P-value: 1.19E-08; mr1810 (All); LR P-value: 3.97E-08; mr1838 (All); LR P-value: 1.89E-21; mr1839 (All); LR P-value: 2.49E-22; mr1886 (All); LR P-value: 1.36E-06; mr1909 (All); LR P-value: 7.36E-16; mr1921 (All); LR P-value: 5.31E-12 |
LOC_Os12g02350.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.568; most accessible tissue: Zhenshan97 flower, score: 78.500 |
| vg1200762080 (J) | chr12 | 762080 | T | A | 92.60% | 0.00% | T -> A |
LOC_Os12g02350.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02370.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02340.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 38.354; most accessible tissue: Zhenshan97 flower, score: 78.500 |
|
| vg1200762105 (J) | chr12 | 762105 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os12g02340.2 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os12g02340.1 Alt: G| stop_retained_variant LOW(snpEff) LOC_Os12g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.4 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 41.081; most accessible tissue: Zhenshan97 flower, score: 80.613 |
| vg1200762108 (J) | chr12 | 762108 | C | A | 99.80% | 0.00% | C -> A | NA |
LOC_Os12g02340.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 41.081; most accessible tissue: Zhenshan97 flower, score: 80.613 |
| vg1200762139 (J) | chr12 | 762139 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os12g02340.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 42.623; most accessible tissue: Zhenshan97 flower, score: 80.159 |
| vg1200762191 (J) | chr12 | 762191 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os12g02340.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os12g02340.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.4 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 48.179; most accessible tissue: Zhenshan97 flower, score: 79.850 |
| vg1200762249 (J) | chr12 | 762249 | C | T | 50.80% | 0.00% | T -> C |
mr1128 (All); LR P-value: 5.00E-10;
mr1172 (All); LR P-value: 1.39E-10; mr1209 (All); LR P-value: 5.90E-06; mr1278 (All); LR P-value: 7.06E-07; mr1302 (All); LR P-value: 1.54E-08; mr1315 (All); LR P-value: 2.10E-06; mr1332 (All); LR P-value: 3.02E-09; mr1336 (All); LR P-value: 3.84E-09; mr1386 (All); LR P-value: 4.86E-12; mr1392 (All); LR P-value: 3.67E-08; mr1442 (All); LR P-value: 2.79E-10; mr1461 (All); LR P-value: 3.11E-06; mr1508 (All); LR P-value: 6.96E-06; mr1579 (All); LR P-value: 3.88E-13; mr1633 (All); LR P-value: 1.22E-06; mr1636 (All); LR P-value: 1.47E-13; mr1646 (All); LR P-value: 3.23E-06; mr1683 (All); LR P-value: 2.14E-13; mr1775 (All); LR P-value: 1.52E-10; mr1776 (All); LR P-value: 1.42E-08; mr1810 (All); LR P-value: 8.08E-09; mr1838 (All); LR P-value: 8.57E-21; mr1839 (All); LR P-value: 2.83E-21; mr1846 (All); LR P-value: 3.22E-11; mr1886 (All); LR P-value: 3.02E-07; mr1909 (All); LR P-value: 2.12E-15; mr1921 (All); LR P-value: 1.56E-11; mr1944 (Ind_All); LR P-value: 3.48E-06; mr1979 (All); LR P-value: 1.21E-06 |
LOC_Os12g02340.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02340.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.078; most accessible tissue: Zhenshan97 flower, score: 82.481 |
| vg1200762296 (J) | chr12 | 762296 | T | G | 92.20% | 0.00% | T -> G |
mr1095 (All); LR P-value: 8.27E-24;
mr1098 (All); LR P-value: 3.51E-32; mr1099 (All); LR P-value: 1.14E-27; mr1101 (All); LR P-value: 1.47E-26; mr1113 (All); LR P-value: 5.55E-15; mr1119 (All); LR P-value: 3.36E-17; mr1240 (All); LR P-value: 4.23E-17; mr1262 (All); LR P-value: 1.42E-06; mr1589 (All); LR P-value: 1.53E-22; mr1649 (All); LR P-value: 1.47E-11; mr1696 (All); LR P-value: 2.47E-10; mr1868 (All); LR P-value: 9.12E-26; mr1911 (All); LR P-value: 2.16E-18; mr1918 (All); LR P-value: 7.84E-13; mr1961 (All); LR P-value: 2.05E-19; mr1095_2 (All); LR P-value: 1.02E-24; mr1098_2 (All); LR P-value: 1.43E-34; mr1099_2 (All); LR P-value: 1.90E-26; mr1123_2 (All); LR P-value: 3.41E-21; mr1240_2 (All); LR P-value: 1.88E-19; mr1409_2 (All); LR P-value: 4.39E-12; mr1762_2 (All); LR P-value: 8.24E-07; mr1911_2 (All); LR P-value: 7.24E-17; mr1918_2 (All); LR P-value: 5.25E-13; mr1936_2 (All); LR P-value: 4.00E-15 |
LOC_Os12g02340.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g02340.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g02370.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.650; most accessible tissue: Zhenshan97 flower, score: 83.061 |
| vg1200762452 (J) | chr12 | 762452 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os12g02340.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os12g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02340.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g02370.4 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.701; most accessible tissue: Zhenshan97 flower, score: 83.283 |