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 mr1486 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
vg1001438303 sf1001437280 10 1438303 4.37E-65 8.78E-25
vg1016395228 sf1016324004 10 16395228 1.44E-44 6.06E-06
vg1001432912 sf1001431889 10 1432912 2.12E-43 2.18E-07
vg0815684621 sf0815681907 8 15684621 3.85E-43 NA
vg1225029132 sf1224995585 12 25029132 1.27E-42 NA
vg0122872464 sf0122871420 1 22872464 8.89E-42 NA
vg0109515272 sf0109514248 1 9515272 8.51E-40 2.90E-06
vg0917940762 sf0917939761 9 17940762 9.07E-40 2.82E-06
vg1001244211 sf1001243188 10 1244211 NA 2.24E-18
vg1001229450 sf1001228427 10 1229450 NA 1.02E-16
vg1001403288 sf1001402265 10 1403288 NA 2.75E-12
vg1001428076 sf1001427053 10 1428076 NA 2.13E-11
vg1001831505 sf1001830482 10 1831505 NA 7.57E-10
vg1001213195 sf1001212172 10 1213195 NA 3.20E-09
vg1002108639 sf1002107616 10 2108639 NA 3.67E-09
vg1000290718 sf1000289718 10 290718 NA 1.07E-08
vg1002287752 sf1002286729 10 2287752 NA 1.20E-08
vg1001467114 sf1001466091 10 1467114 NA 2.51E-08
vg1001440523 sf1001439500 10 1440523 NA 2.81E-08
vg0720057093 sf0720056100 7 20057093 NA 3.31E-08
vg1000080430 sf1000079430 10 80430 NA 1.80E-07
vg1001393945 sf1001392922 10 1393945 NA 4.51E-07
vg0818608910 sf0818606197 8 18608910 NA 4.84E-07
vg0232306661 sf0232300792 2 32306661 NA 5.97E-07
vg0720055978 sf0720054985 7 20055978 NA 1.28E-06
vg0501490301 sf0501490285 5 1490301 NA 1.39E-06
vg0130107774 sf0130106729 1 30107774 NA 1.50E-06
vg1001287549 sf1001286526 10 1287549 NA 1.62E-06
vg1002269285 sf1002268262 10 2269285 NA 2.16E-06
vg1001652766 sf1001651743 10 1652766 NA 2.63E-06
vg1221827817 sf1221794364 12 21827817 NA 2.94E-06
vg0501807710 sf0501807693 5 1807710 NA 3.37E-06