Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1042 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0221812870 sf0221807001 2 21812870 6.32E-43 1.32E-24
vg0141976188 sf0141975145 1 41976188 5.27E-30 1.29E-06
vg1119903744 sf1119437667 11 19903744 1.11E-29 1.96E-07
vg0133276707 sf0133275663 1 33276707 7.58E-29 7.30E-06
vg1015342431 sf1015271199 10 15342431 1.21E-27 8.32E-06
vg0307749732 sf0307748670 3 7749732 1.23E-27 3.95E-08
vg0141963794 sf0141962751 1 41963794 1.92E-26 1.19E-07
vg1119579328 sf1119113016 11 19579328 4.35E-26 1.38E-09
vg0712408577 sf0712407584 7 12408577 1.46E-25 2.02E-06
vg1118063449 sf1117597307 11 18063449 2.23E-25 1.89E-08
vg0212332283 sf0212332279 2 12332283 2.11E-23 1.17E-08
vg1122418723 sf1121952594 11 22418723 4.76E-23 7.12E-07
vg0216188882 sf0216183012 2 16188882 6.48E-23 1.62E-09
vg0221797930 sf0221792061 2 21797930 1.40E-22 2.57E-08
vg1016092335 sf1016021107 10 16092335 7.13E-22 2.67E-08
vg0706728204 sf0706727209 7 6728204 1.02E-21 5.92E-07
vg0234350925 sf0234345056 2 34350925 1.62E-21 1.41E-07
vg0129064779 sf0129063734 1 29064779 2.53E-21 3.63E-07
vg0126344348 sf0126343304 1 26344348 1.54E-20 1.25E-06
vg0620204835 sf0620203838 6 20204835 5.41E-20 NA
vg0430557936 sf0430372811 4 30557936 NA 2.61E-10
vg0221815577 sf0221809708 2 21815577 NA 1.99E-08
vg0211188937 sf0211188934 2 11188937 NA 7.27E-08
vg0221862609 sf0221856740 2 21862609 NA 2.02E-07
vg0221953647 sf0221947778 2 21953647 NA 9.00E-07
vg0212395942 sf0212395938 2 12395942 NA 9.75E-07
vg0315238169 sf0315236816 3 15238169 NA 1.09E-06
vg0132744722 sf0132743678 1 32744722 NA 1.20E-06
vg1206197428 sf1206196319 12 6197428 NA 2.31E-06
vg0300939247 sf0300938245 3 939247 NA 2.86E-06