SNP | Chr. | Position | Alleles | P.value | Bonferroni Corrected | MAF | FDR Adjusted P-values | Nearest Gene | Gene Annotation | Protein Function | Associated Traits |
---|---|---|---|---|---|---|---|---|---|---|---|
S1_10,108,457 | 1 | 10,108,457 | A/G | 5.64E-10 | 3.49E-06 | 0.5281690141 | 0.00000 | LOC104786434 | clavaminate synthase-like protein At3g21360 | metal ion binding; oxidoreductase activity | WE48 |
 |  |  |  | 3.17E-10 | 1.96E-06 |  | 0.00000 |  |  |  | WE46 |
 |  |  |  | 1.12E-06 | 6.93E-03 |  | 0.00346 |  |  |  | WE44 |
 |  |  |  | 2.74E-11 | 1.69E-07 |  | 0.00000 |  |  |  | WE42 |
 |  |  |  | 8.99E-10 | 5.57E-06 |  | 0.00000 |  |  |  | WE_total |
S1_14,592,616 | 1 | 14,592,616 | G/A | 2.24E-06 | 1.39E-02 | 0.1150234742 | 0.00106 | LOC104707605 | uncharacterized | NA | WE_total |
 |  |  |  | 6.92E-07 | 4.28E-03 |  | 0.00043 |  |  |  | AG19 |
S3_25,592,310 | 3 | 25,592,310 | T/C | 1.07E-07 | 6.61E-04 | 0.0915492958 | 0.00008 | LOC104778100 | uncharacterized | NA | WE_total |
 |  |  |  | 3.89E-09 | 2.41E-05 |  | 0.00001 |  |  |  | AG19 |
S5_17,084,259 | 5 | 17,084,259 | A/C | 3.46E-06 | 2.14E-02 | 0.9319248826 | 0.00513 | LOC104789323 | uncharacterized | NA | WE44 |
 |  |  |  | 3.49E-09 | 2.16E-05 |  | 0.00001 |  |  |  | WE42 |
 |  |  |  | 5.48E-08 | 3.40E-04 |  | 0.00005 |  |  |  | WE_total |
 |  |  |  | 3.75E-07 | 2.32E-03 |  | 0.00029 |  |  |  | AG19 |
S5_23,163,110 | 5 | 23,163,110 | A/G | 1.08E-06 | 6.70E-03 | 0.9084507042 | 0.00112 | LOC104789501 | 40S ribosomal protein S11–1-like | RNA binding | WE42 |
 |  |  |  | 6.48E-07 | 4.01E-03 |  | 0.00036 |  |  |  | WE_total |
S5_23,163,133 | 5 | 23,163,133 | A/C | 1.08E-06 | 6.70E-03 | 0.9084507042 | 0.00112 | LOC104789501 | 40S ribosomal protein S11–1-like | RNA binding | WE42 |
 |  |  |  | 6.48E-07 | 4.01E-03 |  | 0.00036 |  |  |  | WE_total |
S5_29,786,454 | 5 | 29,786,454 | T/C | 3.25E-09 | 2.01E-05 | 0.0704225352 | 0.00000 | LOC104789700 | uncharacterized | NA | WE48 |
 |  |  |  | 2.31E-08 | 1.43E-04 |  | 0.00003 |  |  |  | WE46 |
 |  |  |  | 1.32E-06 | 8.19E-03 |  | 0.00068 |  |  |  | WE_total |
S6_7,999,118 | 6 | 7,999,118 | A/G | 3.82E-08 | 2.37E-04 | 0.0046948357 | 0.00024 | LOC104780231 | brefeldin A-inhibited guanine nucleotide-exchange protein 5 | vesicle trafficking, PAMP-triggered immunity (PTI), effector-triggered immunity (ETI), and salicylic acid (SA)-regulated immunity | ALK33 |
 |  |  |  | 9.75E-07 | 6.04E-03 |  | 0.00604 |  |  |  | ALK_total |
S7_24,153,024 | 7 | 24,153,024 | C/T | 1.20E-09 | 7.43E-06 | 0.929577465 | 0.00000 | LOC104704901 | probable purine permease 14 | NA | AG19 |
S7_4,441,246 | 7 | 4,441,246 | T/C | 4.65E-06 | 2.88E-02 | 0.1384976526 | 0.00221 | LOC109125528 | uncharacterized | NA | WE48 |
S7_4,787,171 | 7 | 4,787,171 | A/G | 7.15E-11 | 4.43E-07 | 0.9201877934 | 0.00000 | LOC104700327 | B-box zinc finger protein 25-like | negative regulator of seedling photomorphogenesis | WE48 |
 |  |  |  | 2.58E-09 | 1.60E-05 |  | 0.00000 |  |  |  | WE46 |
 |  |  |  | 1.60E-10 | 9.91E-07 |  | 0.00000 |  |  |  | WE_total |
S7_9,579,071 | 7 | 9,579,071 | G/T | 4.26E-07 | 2.64E-03 | 0.117370892 | 0.00029 | LOC104700816 | uncharacterized | NA | AG19 |
S8_12,332,278 | 8 | 12,332,278 | C/T | 5.84E-07 | 3.62E-03 | 0.765258216 | 0.00090 | LOC109126081 | RNA-directed DNA polymerase homolog | RNA-directed 5′-3′ RNA polymerase activity; RNA-directed DNA polymerase activity | Mar25 |
S8_21,155,371 | 8 | 21,155,371 | C/T | 4.36E-09 | 2.70E-05 | 0.8004694836 | 0.00000 | LOC104709776 | glutathione S-transferase T3-like | conjunction of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles and detoxification against certain herbicides | WE48 |
 |  |  |  | 5.08E-08 | 3.15E-04 |  | 0.00004 |  |  |  | WE46 |
 |  |  |  | 9.12E-07 | 5.64E-03 |  | 0.00112 |  |  |  | WE42 |
 |  |  |  | 3.98E-06 | 2.47E-02 |  | 0.00164 |  |  |  | WE_total |
S8_23,054,597 | 8 | 23,054,597 | T/C | 2.07E-06 | 1.28E-02 | 0.061032864 | 0.00107 | LOC104709847 | cytochrome P450 81D1-like (pseudo) | metal binding | AG19 |
S8_5,912,798 | 8 | 5,912,798 | A/C | 6.67E-06 | 4.13E-02 | 0.9084507042 | 0.00283 | LOC104706385 | uro-adherence factor A-like | cell wall anchored protein--erythrocyte binding activity | WE48 |
 |  |  |  | 5.83E-06 | 3.61E-02 |  | 0.00226 |  |  |  | WE_total |
S9_7,943,388 | 9 | 7,943,388 | A/G | 3.68E-06 | 2.28E-02 | 0.9014084507 | 0.00190 | LOC104710709 | protein arginine methyltransferase NDUFAF7 homolog, mitochondrial | assembly or stability of mitochondrial NADH:ubiquinone oxidoreductase complex | WE48 |
S11_13,254,172 | 11 | 13,254,172 | T/G | 6.98E-06 | 4.32E-02 | 0.0633802817 | 0.00393 | LOC109124846 | vacuolar protein sorting-associated protein 25-like | delivery of transmembrane proteins into the lumen of the lysosome for degradation | WE46 |
S11_47,072,592 | 11 | 47,072,592 | A/G | 1.17E-06 | 7.27E-03 | 0.9014084507 | 0.00073 | LOC104726883 | peroxisomal membrane protein PEX14 | peroxisome movement | WE48 |
 |  |  |  | 3.33E-06 | 2.06E-02 |  | 0.01032 |  |  |  | ALC32 |
 |  |  |  | 3.68E-08 | 2.28E-04 |  | 0.00011 |  |  |  | ALC34 |
 |  |  |  | 2.61E-07 | 1.62E-03 |  | 0.00081 |  |  |  | ALD30 |
S11_47,072,593 | 11 | 47,072,593 | A/T | 1.17E-06 | 7.27E-03 | Â | 0.00073 | Â | Â | Â | WE48 |
S11_49,518,817 | 11 | 49,518,817 | C/T | 4.14E-06 | 2.57E-02 | 0.6267605634 | 0.00513 | LOC104727408 | GATA transcription factor 5-like | regulation of some light-responsive genes | WE44 |
S12_10,333,667 | 12 | 10,333,667 | C/G | 3.76E-10 | 2.33E-06 | 0.9460093897 | 0.00000 | LOC104731181 | glutamate--cysteine ligase, chloroplastic-like | resistance to fungal and bacterial pathogens-regulation of salicylic acid (SA) and phytoalexin (camalexin) production. | WE48 |
 |  |  |  | 1.97E-10 | 1.22E-06 |  | 0.00000 |  |  |  | WE46 |
 |  |  |  | 1.68E-06 | 1.04E-02 |  | 0.00347 |  |  |  | WE44 |
 |  |  |  | 4.13E-11 | 2.56E-07 |  | 0.00000 |  |  |  | WE_total |
 |  |  |  | 1.26E-06 | 7.80E-03 |  | 0.00071 |  |  |  | AG19 |
S12_20,455,684 | 12 | 20,455,684 | G/A | 2.72E-07 | 1.68E-03 | 0.1408450704 | 0.00056 | LOC104732333 | uncharacterized | NA | Mar25 |
S12_9,157,483 | 12 | 9,157,483 | G/T | 2.39E-06 | 1.48E-02 | 0.8920187793 | 0.00106 | LOC104731044 | kinesin-like protein KIN-7I | somatic cell cytokinesis, cell-plate formation and its expansion | WE_total |
S13_1,532,622 | 13 | 1,532,622 | G/A | 6.46E-06 | 4.00E-02 | 0.7699530516 | 0.00400 | LOC104734437 | probable lysine-specific demethylase ELF6 | transcriptional gene regulation; repressor of the photoperiodic flowering pathway and of FT. | Mar25 |
S13_21,456,713 | 13 | 21,456,713 | A/G | 1.70E-06 | 1.05E-02 | 0.7769953052 | 0.00211 | LOC104738457 | uncharacterized | NA | Mar25 |
S13_5,037,723 | 13 | 5,037,723 | C/A | 6.43E-07 | 3.98E-03 | 0.0751173709 | 0.00112 | LOC104735215 | U-box domain-containing protein 52-like | protein ubiquitination | WE42 |
S15_11,699,414 | 15 | 11,699,414 | C/T | 2.51E-09 | 1.55E-05 | 0.896713615 | 0.00002 | LOC104746477 | uncharacterized | NA | Mar25 |
S15_25,879,428 | 15 | 25,879,428 | C/T | 2.44E-06 | 1.51E-02 | 0.9107981221 | 0.00137 | LOC104748799 | uncharacterized | NA | WE48 |
 |  |  |  | 5.39E-06 | 3.34E-02 |  | 0.00334 |  |  |  | WE46 |
 |  |  |  | 1.85E-07 | 1.14E-03 |  | 0.00013 |  |  |  | WE_total |
S16_10,454,057 | 16 | 10,454,057 | T/C | 2.37E-06 | 1.47E-02 | 0.1103286385 | 0.00210 | LOC104750305 | ERAD-associated E3 ubiquitin-protein ligase HRD1B-like | protein ubiquitination | WE42 |
S16_11,083,391 | 16 | 11,083,391 | C/T | 8.64E-10 | 5.35E-06 | 0.931924883 | 0.00000 | LOC104750339 | leucine-rich repeat receptor-like protein CLAVATA2 | membrane component | AG19 |
S16_2,915,369 | 16 | 2,915,369 | T/C | 6.87E-07 | 4.25E-03 | 0.1009389671 | 0.00425 | LOC104749495 | DEAD-box ATP-dependent RNA helicase 21-like | ribosome biogenesis, mRNA degradation and translation initiation. | ALC26 |
S16_9,912,650 | 16 | 9,912,650 | T/C | 1.31E-07 | 8.11E-04 | 0.112676056 | 0.00012 | LOC104753537 | uncharacterized | NA | AG19 |
S16_9,912,651 | 16 | 9,912,651 | G/A | 7.71E-08 | 4.77E-04 | 0.08685446 | 0.00010 | LOC104753537 | uncharacterized | NA | AG19 |
S16_9,912,652 | 16 | 9,912,652 | G/A | 1.31E-07 | 8.11E-04 | 0.112676056 | 0.00012 | LOC104753537 | uncharacterized | NA | AG19 |
S17_32,490,691 | 17 | 32,490,691 | T/A | 2.56E-11 | 1.59E-07 | 0.0704225352 | 0.00000 | LOC104758647 | protein SPA1-RELATED 4-like | Repressor of photomorphogenesis in the blue light | WE48 |
 |  |  |  | 7.71E-11 | 4.77E-07 |  | 0.00000 |  |  |  | WE46 |
 |  |  |  | 1.02E-06 | 6.32E-03 |  | 0.00346 |  |  |  | WE44 |
 |  |  |  | 4.17E-12 | 2.58E-08 |  | 0.00000 |  |  |  | WE_total |
 |  |  |  | 3.65E-07 | 2.26E-03 |  | 0.00226 |  |  |  | ALK35 |
 |  |  |  | 1.46E-09 | 9.04E-06 |  | 0.00000 |  |  |  | AG19 |
S17_33,558,126 | 17 | 33,558,126 | A/T | 7.83E-10 | 4.85E-06 | 0.8849765258 | 0.00000 | LOC104758812 | probable acyl-activating enzyme 18, peroxisomal | peroxisomal activation of 2,4-dichlorophenoxybutyric acid (2,4-dB) | WE48 |
 |  |  |  | 2.97E-08 | 1.84E-04 |  | 0.00003 |  |  |  | WE46 |
 |  |  |  | 2.23E-08 | 1.38E-04 |  | 0.00002 |  |  |  | WE_total |
S17_3,778,452 | 17 | 3,778,452 | A/G | 2.77E-06 | 1.71E-02 | 0.882629108 | 0.00214 | LOC104755111 | U11NAU12 small nuclear ribonucleoprotein 65 kDa protein | branch-point site recognition for normal plant development | WE42 |
 |  |  |  | 5.08E-06 | 3.15E-02 |  | 0.00242 |  |  |  | AG19 |
S18_2,191,451 | 18 | 2,191,451 | C/A | 6.97E-06 | 4.32E-02 | 0.3755868545 | 0.04316 | LOC104760305 | WUSCHEL-related homeobox 8-like | basal embryo development after fertilization | ALC_total |
S19_10,881,936 | 19 | 10,881,936 | G/C | 6.85E-06 | 4.24E-02 | 0.103286385 | 0.00283 | LOC104765950 | F-box protein At5g07610-like | NA | WE48 |
 |  |  |  | 2.56E-06 | 1.59E-02 |  | 0.00176 |  |  |  | WE46 |
 |  |  |  | 3.63E-06 | 2.24E-02 |  | 0.00249 |  |  |  | WE42 |
S19_19,179,520 | 19 | 19,179,520 | G/T | 4.70E-09 | 2.91E-05 | 0.8708920188 | 0.00000 | LOC109131004 | histone deacetylase 6-like | protein deacetylase activity; degradation of misfoleded proteins | WE48 |
 |  |  |  | 1.61E-07 | 9.99E-04 |  | 0.00012 |  |  |  | WE46 |
 |  |  |  | 1.57E-09 | 9.73E-06 |  | 0.00000 |  |  |  | WE_total |
S19_4,005,938 | 19 | 4,005,938 | C/G | 2.19E-06 | 1.36E-02 | 0.8544600939 | 0.00735 | LOC104764661 | probable DNA helicase MCM8 (pseudo) | DNA repair during meiosis | AG23 |
 |  |  |  | 2.21E-06 | 1.37E-02 |  | 0.00228 |  |  |  | MAR25 |
S20_6,023,906 | 20 | 6,023,906 | G/A | 1.59E-08 | 9.85E-05 | 0.1408450704 | 0.00005 | LOC104769581 | magnesium-chelatase subunit ChlH, chloroplastic | chlorophyll synthesis,plastid-to-nucleus retrograde signaling and abscisic acid (ABA) perception | MAR25 |