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 mr1918 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
vg0222743508 sf0222737639 2 22743508 8.25E-58 1.55E-43
vg0222725905 sf0222720036 2 22725905 1.20E-57 6.35E-45
vg0223078170 sf0223072301 2 23078170 2.06E-16 1.76E-10
vg0223079116 sf0223073247 2 23079116 2.67E-15 1.98E-09
vg0221717789 sf0221711920 2 21717789 3.71E-15 4.27E-08
vg0221658331 sf0221652462 2 21658331 1.46E-13 1.75E-07
vg0223663745 sf0223657876 2 23663745 6.01E-13 7.24E-11
vg0223027242 sf0223021373 2 23027242 6.04E-13 4.56E-06
vg0222634177 sf0222628308 2 22634177 6.77E-13 2.51E-07
vg0224622358 sf0224616489 2 24622358 9.19E-13 5.13E-06
vg1112606104 sf1112142307 11 12606104 1.58E-10 3.46E-07
vg0222799001 sf0222793132 2 22799001 1.83E-10 9.24E-08
vg0222879623 sf0222873754 2 22879623 3.20E-10 3.17E-13
vg0222681985 sf0222676116 2 22681985 5.03E-10 9.21E-12
vg0224678754 sf0224672885 2 24678754 6.66E-10 3.49E-06
vg0222672641 sf0222666772 2 22672641 1.71E-09 1.09E-06
vg0223072760 sf0223066891 2 23072760 3.60E-09 7.08E-08
vg0224274396 sf0224268527 2 24274396 7.94E-09 3.34E-07
vg0224832469 sf0224826600 2 24832469 4.09E-07 6.51E-08
vg0222546026 sf0222540157 2 22546026 NA 8.98E-07
vg0525239875 sf0525177296 5 25239875 NA 1.36E-06
vg0224736708 sf0224730839 2 24736708 NA 2.25E-06
vg0223036991 sf0223031122 2 23036991 NA 4.23E-06