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 mr1835 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
vg1102103286 sf1102099144 11 2103286 1.61E-13 1.29E-06
vg0528031260 sf0527968615 5 28031260 5.51E-12 NA
vg0700618041 sf0700617041 7 618041 1.96E-11 NA
vg0234625806 sf0234619937 2 34625806 7.61E-10 NA
vg1122732664 sf1122266535 11 22732664 1.02E-09 NA
vg1125785739 sf1125319578 11 25785739 2.45E-09 1.46E-06
vg0812013581 sf0812012586 8 12013581 1.38E-08 2.73E-06
vg0812296238 sf0812295243 8 12296238 2.15E-08 4.53E-06
vg0811930717 sf0811929722 8 11930717 2.79E-08 2.86E-06
vg0810945945 sf0810944950 8 10945945 3.29E-08 1.22E-07
vg0407782064 sf0407777332 4 7782064 1.09E-07 2.66E-08
vg1217064594 sf1217058549 12 17064594 1.14E-07 2.60E-06
vg0812056816 sf0812055821 8 12056816 8.05E-07 5.20E-07
vg0207251260 sf0207251260 2 7251260 2.58E-06 NA
vg0909755639 sf0909754638 9 9755639 3.96E-06 NA
vg1203644489 sf1203643488 12 3644489 4.51E-06 NA
vg0402393980 sf0402389575 4 2393980 NA 1.55E-06
vg0402465952 sf0402461550 4 2465952 NA 1.71E-06
vg0402671824 sf0402667428 4 2671824 NA 3.27E-06
vg0701737366 sf0701736367 7 1737366 NA 3.34E-06
vg1217374273 sf1217368228 12 17374273 NA 3.47E-06
vg0712512342 sf0712511349 7 12512342 NA 4.45E-06