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 mr1163 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
vg0433811482 sf0433626370 4 33811482 1.79E-27 8.25E-11
vg0204007916 sf0204007913 2 4007916 1.93E-26 NA
vg0131676504 sf0131675460 1 31676504 7.87E-26 5.20E-06
vg0434058002 sf0433872894 4 34058002 1.49E-25 NA
vg0113350301 sf0113349275 1 13350301 2.28E-25 NA
vg0803457136 sf0803456139 8 3457136 4.66E-24 3.35E-06
vg0227395695 sf0227389826 2 27395695 5.12E-24 9.78E-08
vg0136395808 sf0136394765 1 36395808 8.06E-24 1.63E-07
vg0133208151 sf0133207107 1 33208151 8.33E-24 3.05E-07
vg0824901602 sf0824898888 8 24901602 1.18E-23 1.30E-06
vg0122505956 sf0122504911 1 22505956 2.04E-23 4.22E-06
vg0425465226 sf0425280086 4 25465226 2.05E-23 3.16E-06
vg0229928131 sf0229922262 2 29928131 3.52E-23 3.69E-06
vg0204087549 sf0204087546 2 4087549 3.95E-23 4.22E-06
vg0139256874 sf0139255831 1 39256874 4.69E-23 1.21E-07
vg0526919672 sf0526857029 5 26919672 1.03E-22 3.45E-08
vg0307479900 sf0307478838 3 7479900 5.37E-22 3.37E-07
vg1201615762 sf1201614762 12 1615762 7.00E-22 1.78E-07
vg0526919176 sf0526856533 5 26919176 NA 1.10E-07
vg1208708611 sf1208706018 12 8708611 NA 2.86E-07
vg0700211553 sf0700210553 7 211553 NA 3.87E-07
vg0211842905 sf0211842901 2 11842905 NA 5.72E-07
vg0137912344 sf0137911301 1 37912344 NA 1.22E-06
vg1110106704 sf1110101281 11 10106704 NA 1.76E-06
vg0719604554 sf0719603561 7 19604554 NA 2.63E-06
vg0700603684 sf0700602684 7 603684 NA 3.08E-06
vg1215235888 sf1218062462 12 15235888 NA 3.46E-06
vg0813113439 sf0813110999 8 13113439 NA 3.60E-06