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 mr1841 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
vg1125118463 sf1124652303 11 25118463 4.80E-29 1.37E-30
vg1124875808 sf1124409648 11 24875808 9.69E-13 1.74E-15
vg1124991220 sf1124525060 11 24991220 4.77E-09 4.22E-14
vg1124914537 sf1124448377 11 24914537 6.98E-09 1.93E-14
vg1128437977 sf1127914756 11 28437977 8.74E-09 NA
vg1124970141 sf1124503981 11 24970141 1.61E-08 2.66E-07
vg1124959837 sf1124493677 11 24959837 2.42E-08 1.65E-07
vg1125022392 sf1124556232 11 25022392 1.87E-07 3.47E-07
vg0721634662 sf0721633669 7 21634662 7.86E-07 6.29E-07
vg0814644208 sf0814641494 8 14644208 1.20E-06 2.94E-06
vg1124931687 sf1124465527 11 24931687 1.44E-06 1.84E-09
vg1125525722 sf1125059561 11 25525722 3.61E-06 3.28E-06
vg0328637867 sf0328630920 3 28637867 4.95E-06 3.32E-06
vg1122501574 sf1122035445 11 22501574 7.21E-06 3.45E-06
vg1125038779 sf1124572619 11 25038779 9.37E-06 2.82E-08
vg0208287795 sf0208287794 2 8287795 NA 7.37E-07
vg1124948132 sf1124481972 11 24948132 NA 8.29E-07
vg1124975706 sf1124509546 11 24975706 NA 2.13E-06
vg0907106741 sf0907105741 9 7106741 NA 2.37E-06
vg1122485909 sf1122019780 11 22485909 NA 2.74E-06
vg0901835907 sf0901834907 9 1835907 NA 3.01E-06
vg0106089280 sf0106088280 1 6089280 NA 4.24E-06