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 mr1871 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 4.72E-67 2.99E-45
vg1117896001 sf1117429859 11 17896001 1.31E-34 1.85E-09
vg0133296558 sf0133295514 1 33296558 5.28E-34 2.86E-06
vg0307762603 sf0307761541 3 7762603 2.13E-32 1.82E-09
vg0141963794 sf0141962751 1 41963794 2.81E-32 1.80E-11
vg1114800054 sf1114336368 11 14800054 1.28E-30 7.93E-09
vg1118063449 sf1117597307 11 18063449 1.24E-29 1.32E-09
vg1119577611 sf1119111299 11 19577611 4.11E-29 2.43E-11
vg0216188882 sf0216183012 2 16188882 1.56E-28 6.44E-14
vg1122418723 sf1121952594 11 22418723 3.14E-28 6.74E-10
vg0129151653 sf0129150608 1 29151653 3.56E-28 1.16E-09
vg0809845346 sf0809844350 8 9845346 1.89E-27 9.31E-10
vg0212332283 sf0212332279 2 12332283 2.30E-27 1.24E-11
vg1107886187 sf1107881932 11 7886187 1.87E-26 1.41E-10
vg1121977578 sf1121511449 11 21977578 4.21E-25 1.67E-08
vg0629150340 sf0629149342 6 29150340 1.63E-24 9.78E-11
vg1019934319 sf1019862819 10 19934319 6.18E-23 1.79E-08
vg0222465672 sf0222459803 2 22465672 1.38E-22 7.16E-11
vg0221797930 sf0221792061 2 21797930 1.86E-21 1.79E-09
vg0105523729 sf0105522729 1 5523729 3.62E-20 NA
vg0430561661 sf0430376536 4 30561661 NA 3.12E-12
vg0221815577 sf0221809708 2 21815577 NA 1.19E-10
vg0134495271 sf0134494228 1 34495271 NA 7.12E-10
vg0430594199 sf0430409074 4 30594199 NA 9.97E-10
vg0212395942 sf0212395938 2 12395942 NA 1.78E-09
vg1126293762 sf1125813126 11 26293762 NA 3.20E-09
vg0402221211 sf0402216806 4 2221211 NA 1.86E-08
vg0402121041 sf0402116635 4 2121041 NA 8.94E-08