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 mr1622 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
vg0207916436 sf0207916435 2 7916436 9.95E-09 6.34E-08
vg0620513077 sf0620512080 6 20513077 9.96E-08 5.94E-07
vg0914107945 sf0914106944 9 14107945 2.72E-07 3.61E-06
vg1007896788 sf1007912398 10 7896788 7.12E-07 6.65E-07
vg1128246741 sf1127723520 11 28246741 9.14E-07 3.04E-08
vg1128246115 sf1127722894 11 28246115 1.30E-06 3.35E-08
vg1125525827 sf1125059666 11 25525827 NA 1.03E-07
vg1222354382 sf1222320821 12 22354382 NA 1.35E-07
vg0220330014 sf0220324146 2 20330014 NA 1.41E-07
vg0207916446 sf0207916445 2 7916446 NA 1.60E-07
vg0728942008 sf0728941016 7 28942008 NA 2.34E-07
vg0520505270 sf0520442741 5 20505270 NA 6.65E-07
vg0131005077 sf0131004033 1 31005077 NA 1.14E-06
vg0709134172 sf0709133178 7 9134172 NA 1.27E-06
vg0921842785 sf0921842304 9 21842785 NA 1.44E-06
vg0317240479 sf0317239289 3 17240479 NA 1.96E-06
vg0517977755 sf0517917241 5 17977755 NA 2.26E-06
vg0130092159 sf0130091114 1 30092159 NA 3.02E-06
vg0920309441 sf0920308960 9 20309441 NA 3.31E-06
vg1017701795 sf1017630568 10 17701795 NA 3.88E-06