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 mr1672 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
vg0138163545 sf0138162502 1 38163545 3.85E-161 2.10E-23
vg0137988430 sf0137987387 1 37988430 1.32E-160 2.49E-24
vg1119381446 sf1118915134 11 19381446 2.54E-127 NA
vg0631238601 sf0631237603 6 31238601 2.48E-124 NA
vg0221095386 sf0221089518 2 21095386 8.92E-123 NA
vg1101376555 sf1101375556 11 1376555 1.46E-122 NA
vg0400468558 sf0400467556 4 468558 NA 2.11E-27
vg0400454931 sf0400453929 4 454931 NA 2.72E-25
vg0400441010 sf0400440008 4 441010 NA 4.14E-21
vg0400440847 sf0400439845 4 440847 NA 1.46E-15
vg0400445622 sf0400444620 4 445622 NA 1.00E-12
vg0400439210 sf0400438208 4 439210 NA 1.55E-11
vg1020393351 sf1020321831 10 20393351 NA 1.71E-09
vg0400438884 sf0400437882 4 438884 NA 6.35E-09
vg0628049712 sf0628048714 6 28049712 NA 3.58E-08
vg0400377457 sf0400376455 4 377457 NA 4.78E-08
vg0220315567 sf0220309699 2 20315567 NA 8.34E-08
vg0400066292 sf0400065292 4 66292 NA 1.59E-07
vg0815510507 sf0815507793 8 15510507 NA 1.96E-07
vg0142104276 sf0142103233 1 42104276 NA 2.31E-07
vg0700117506 sf0700116506 7 117506 NA 2.69E-07
vg0305205234 sf0305204234 3 5205234 NA 2.72E-07
vg0820974361 sf0820971648 8 20974361 NA 2.74E-07
vg0505502303 sf0505502281 5 5502303 NA 5.58E-07
vg1121246644 sf1120780522 11 21246644 NA 5.88E-07
vg0707143185 sf0707142190 7 7143185 NA 6.73E-07
vg0330850428 sf0330843315 3 30850428 NA 8.64E-07
vg1107619564 sf1107615309 11 7619564 NA 9.76E-07