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 mr1697 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
vg0709448532 sf0709447538 7 9448532 2.76E-08 2.76E-08
vg0420711795 sf0420539838 4 20711795 4.41E-08 4.41E-08
vg0717125545 sf0717124552 7 17125545 2.07E-07 2.07E-07
vg0421031577 sf0420859630 4 21031577 3.71E-07 3.72E-07
vg0421031215 sf0420859268 4 21031215 4.90E-07 4.90E-07
vg0223522667 sf0223516798 2 23522667 7.42E-07 7.42E-07
vg0805826839 sf0805825842 8 5826839 7.75E-07 7.76E-07
vg0704732672 sf0704731673 7 4732672 8.49E-07 8.49E-07
vg0307897988 sf0307896926 3 7897988 8.82E-07 8.82E-07
vg0623981969 sf0623980972 6 23981969 9.75E-07 9.75E-07
vg0421384856 sf0421212909 4 21384856 1.03E-06 1.03E-06
vg0403204105 sf0403199708 4 3204105 1.11E-06 1.11E-06
vg0713442761 sf0713441768 7 13442761 1.37E-06 1.37E-06
vg0516508609 sf0516451091 5 16508609 1.53E-06 1.53E-06
vg0424181194 sf0423996055 4 24181194 2.26E-06 2.26E-06
vg0902278490 sf0902277490 9 2278490 2.57E-06 2.57E-06
vg0921004343 sf0921003862 9 21004343 3.21E-06 3.21E-06
vg0612179300 sf0612178301 6 12179300 3.74E-06 3.74E-06
vg0521872068 sf0521809510 5 21872068 3.74E-06 3.74E-06
vg1208774850 sf1208772257 12 8774850 4.42E-06 4.42E-06
vg0403140954 sf0403136557 4 3140954 4.68E-06 4.68E-06