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 mr1133 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
vg1125494322 sf1125028161 11 25494322 4.41E-34 7.43E-19
vg1125492809 sf1125026648 11 25492809 1.79E-33 1.37E-19
vg0713261979 sf0713260986 7 13261979 1.94E-22 1.11E-08
vg0713262120 sf0713261127 7 13262120 6.59E-21 1.71E-09
vg0612546146 sf0612545147 6 12546146 6.43E-17 3.33E-08
vg1123611068 sf1123144938 11 23611068 6.45E-16 1.76E-07
vg0612544928 sf0612543929 6 12544928 2.29E-15 1.17E-09
vg1127656211 sf1127184598 11 27656211 4.45E-15 1.02E-06
vg1127580369 sf1127108756 11 27580369 1.40E-14 1.75E-07
vg1125401366 sf1124935205 11 25401366 2.09E-10 3.66E-06
vg1125393107 sf1124926946 11 25393107 2.45E-10 2.85E-07
vg1125580754 sf1125114593 11 25580754 7.00E-10 1.33E-07
vg1126223931 sf1125752345 11 26223931 2.38E-09 4.32E-06
vg1018062714 sf1017991485 10 18062714 8.94E-09 NA
vg1124843037 sf1124376877 11 24843037 1.68E-08 4.35E-06
vg1124078354 sf1123612224 11 24078354 2.52E-08 1.76E-07
vg1126329911 sf1125858324 11 26329911 3.13E-08 3.77E-07
vg0817496253 sf0817493539 8 17496253 4.95E-08 1.27E-06
vg1125165630 sf1124699470 11 25165630 1.33E-07 4.16E-06
vg1124331154 sf1123865024 11 24331154 3.74E-07 4.22E-06
vg1125603546 sf1125137385 11 25603546 3.92E-07 4.42E-07
vg1125148463 sf1124682303 11 25148463 NA 7.10E-08
vg0310570687 sf0310569603 3 10570687 NA 4.31E-06