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 mr1644 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
vg1125545020 sf1125078859 11 25545020 7.10E-59 1.74E-42
vg1125160316 sf1124694156 11 25160316 3.10E-26 9.64E-23
vg1125669845 sf1125203684 11 25669845 4.11E-23 1.18E-16
vg1125897494 sf1125431413 11 25897494 7.37E-22 1.01E-19
vg0204430393 sf0204430390 2 4430393 9.73E-19 1.31E-14
vg1125897473 sf1125431392 11 25897473 4.90E-17 1.07E-16
vg0507714473 sf0507714414 5 7714473 1.10E-16 1.82E-10
vg1125253130 sf1124786970 11 25253130 1.91E-16 1.02E-20
vg1125163575 sf1124697415 11 25163575 9.83E-16 1.00E-13
vg1124998850 sf1124532690 11 24998850 5.02E-14 1.47E-10
vg1125569375 sf1125103214 11 25569375 7.71E-14 5.44E-13
vg1125245628 sf1124779468 11 25245628 1.46E-13 3.15E-08
vg1204309286 sf1204308274 12 4309286 1.06E-12 1.58E-08
vg0224605253 sf0224599384 2 24605253 2.61E-12 1.67E-11
vg1125839534 sf1125373453 11 25839534 2.76E-12 1.51E-08
vg1125639786 sf1125173625 11 25639786 1.70E-11 1.08E-08
vg1126538466 sf1126066881 11 26538466 3.03E-11 8.89E-09
vg1125862812 sf1125396731 11 25862812 8.71E-11 8.64E-10
vg1125614482 sf1125148321 11 25614482 1.75E-10 9.56E-14
vg0603519050 sf0603518051 6 3519050 4.95E-10 7.60E-08
vg0515506202 sf0515448743 5 15506202 6.68E-10 7.31E-09
vg0525036702 sf0524974117 5 25036702 7.14E-09 1.87E-09
vg1126074837 sf1125603251 11 26074837 2.11E-06 7.04E-08
vg1220752532 sf1220719080 12 20752532 5.77E-06 NA