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 mr1103 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
vg0719067465 sf0719066472 7 19067465 5.83E-22 3.76E-21
vg0719006525 sf0719005532 7 19006525 5.97E-22 3.11E-21
vg0719055987 sf0719054994 7 19055987 8.63E-22 2.30E-25
vg0719056561 sf0719055568 7 19056561 1.83E-20 1.33E-25
vg0107214556 sf0107213556 1 7214556 2.45E-10 1.49E-06
vg0107198487 sf0107197487 1 7198487 3.20E-10 9.25E-07
vg1101911438 sf1101910439 11 1911438 4.20E-09 5.30E-09
vg0408294186 sf0408289460 4 8294186 5.45E-09 1.00E-07
vg0912061274 sf0912060273 9 12061274 6.60E-09 1.77E-06
vg0408293770 sf0408289044 4 8293770 6.71E-09 8.65E-08
vg0907121871 sf0907120871 9 7121871 1.96E-08 6.42E-07
vg0700416280 sf0700415280 7 416280 9.39E-08 4.80E-07
vg0820065663 sf0820062950 8 20065663 9.96E-08 2.98E-07
vg0200846970 sf0200846970 2 846970 2.53E-07 1.80E-06
vg0113106767 sf0113105741 1 13106767 1.35E-06 3.20E-06
vg0828152822 sf0828150108 8 28152822 1.69E-06 3.83E-06
vg0230093704 sf0230087835 2 30093704 2.11E-06 4.72E-06
vg0804028565 sf0804027568 8 4028565 NA 4.88E-07
vg0705107520 sf0705106521 7 5107520 NA 1.05E-06
vg0828401472 sf0828398758 8 28401472 NA 2.24E-06
vg0913971290 sf0913970289 9 13971290 NA 3.09E-06
vg0435372935 sf0435187817 4 35372935 NA 3.29E-06
vg0622666708 sf0622665711 6 22666708 NA 3.93E-06
vg0901474384 sf0901473384 9 1474384 NA 4.16E-06