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 mr1071 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
vg0406526555 sf0406521998 4 6526555 7.88E-172 2.18E-43
vg0411344776 sf0411335479 4 11344776 1.50E-127 NA
vg0307375905 sf0307374903 3 7375905 1.36E-125 1.91E-06
vg1017228554 sf1017157327 10 17228554 1.81E-124 2.72E-06
vg0122842459 sf0122841415 1 22842459 1.01E-121 NA
vg1016499839 sf1016428612 10 16499839 3.07E-117 5.25E-08
vg0412479470 sf0412470185 4 12479470 1.38E-104 6.24E-08
vg0406521772 sf0406517215 4 6521772 NA 1.93E-15
vg0406362113 sf0406357553 4 6362113 NA 2.65E-11
vg0406532594 sf0406528037 4 6532594 NA 6.82E-11
vg0407565723 sf0407560992 4 7565723 NA 7.45E-11
vg0411635497 sf0411626203 4 11635497 NA 2.93E-10
vg0817329442 sf0817326728 8 17329442 NA 2.03E-09
vg0406147466 sf0406142906 4 6147466 NA 3.59E-09
vg0912877788 sf0912876787 9 12877788 NA 1.04E-08
vg0406537255 sf0406532698 4 6537255 NA 1.13E-08
vg1216555105 sf1216552398 12 16555105 NA 1.99E-08
vg1216568179 sf1216565472 12 16568179 NA 3.23E-08
vg0125080782 sf0125079738 1 25080782 NA 3.33E-08
vg1209907443 sf1209904853 12 9907443 NA 5.64E-08
vg1012004873 sf1011933688 10 12004873 NA 8.05E-08
vg0406527348 sf0406522791 4 6527348 NA 1.09E-07
vg0806199663 sf0806198668 8 6199663 NA 1.41E-07
vg1216535929 sf1216533222 12 16535929 NA 1.68E-07
vg0714633836 sf0714632843 7 14633836 NA 1.86E-07
vg0807832561 sf0807831565 8 7832561 NA 9.01E-06