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 mr1739 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
vg0802209035 sf0802208038 8 2209035 1.13E-65 9.72E-37
vg0802232200 sf0802231203 8 2232200 1.43E-63 5.79E-37
vg0802168597 sf0802167600 8 2168597 8.86E-53 4.57E-29
vg0802075324 sf0802074327 8 2075324 9.37E-21 1.81E-10
vg0801819951 sf0801818954 8 1819951 3.88E-20 2.47E-09
vg0801451645 sf0801450647 8 1451645 1.52E-18 2.70E-07
vg0801447167 sf0801446169 8 1447167 6.18E-18 4.00E-06
vg0801912287 sf0801911290 8 1912287 2.60E-17 7.83E-09
vg0114026298 sf0114025272 1 14026298 1.19E-14 4.43E-06
vg0802068171 sf0802067174 8 2068171 5.90E-14 9.06E-09
vg1216034987 sf1216032283 12 16034987 3.76E-12 4.81E-07
vg0802411059 sf0802410062 8 2411059 2.85E-11 2.49E-07
vg0801759737 sf0801758740 8 1759737 8.16E-08 2.49E-06
vg0304633825 sf0304632827 3 4633825 NA 8.88E-08
vg1120458011 sf1119991936 11 20458011 NA 2.96E-06
vg1010028847 sf1009957668 10 10028847 NA 4.00E-06