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 mr1055 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
vg1215966147 sf1215963443 12 15966147 1.04E-53 4.36E-33
vg1215955784 sf1215953080 12 15955784 1.04E-53 4.36E-33
vg0500829493 sf0500829475 5 829493 1.63E-19 NA
vg1212877317 sf1212874656 12 12877317 2.02E-19 3.03E-08
vg0630798684 sf0630797686 6 30798684 3.72E-18 NA
vg1110282765 sf1110277342 11 10282765 2.06E-17 5.14E-06
vg1218663003 sf1218634438 12 18663003 4.80E-15 3.02E-12
vg0919099872 sf0919099461 9 19099872 6.01E-14 1.11E-07
vg1006587700 sf1006603323 10 6587700 1.18E-13 1.21E-10
vg1215852700 sf1215849996 12 15852700 NA 8.89E-17
vg1022588644 sf1022517118 10 22588644 NA 5.98E-11
vg0408293903 sf0408289177 4 8293903 NA 5.89E-09
vg0901555680 sf0901554680 9 1555680 NA 7.97E-09
vg0816293722 sf0816291008 8 16293722 NA 9.52E-09
vg0715496678 sf0715495685 7 15496678 NA 9.60E-09
vg1121327044 sf1120860921 11 21327044 NA 1.11E-08
vg1213186520 sf1213183858 12 13186520 NA 1.54E-08
vg1211633613 sf1211630949 12 11633613 NA 1.89E-08
vg1121318063 sf1120851941 11 21318063 NA 3.04E-08
vg0623791757 sf0623790760 6 23791757 NA 6.24E-08
vg1108620178 sf1108614788 11 8620178 NA 3.50E-07
vg0921818323 sf0921817842 9 21818323 NA 3.53E-07
vg0820168380 sf0820165667 8 20168380 NA 3.92E-07
vg1011512046 sf1011440865 10 11512046 NA 5.04E-07
vg0921889942 sf0921889461 9 21889942 NA 2.29E-06