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 mr1309 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 5.84E-56 1.83E-38
vg0704627367 sf0704626368 7 4627367 8.69E-34 1.44E-10
vg0523113744 sf0523051185 5 23113744 3.98E-33 NA
vg0801536655 sf0801535657 8 1536655 7.50E-33 9.86E-06
vg1017211211 sf1017139984 10 17211211 2.94E-32 NA
vg1125063819 sf1124597659 11 25063819 3.00E-27 1.89E-09
vg1124875808 sf1124409648 11 24875808 7.76E-27 3.38E-14
vg1124989458 sf1124523298 11 24989458 NA 2.22E-22
vg1124986792 sf1124520632 11 24986792 NA 4.49E-18
vg1125120298 sf1124654138 11 25120298 NA 1.57E-17
vg1125080303 sf1124614143 11 25080303 NA 2.97E-13
vg1125113390 sf1124647230 11 25113390 NA 1.26E-12
vg1125233443 sf1124767283 11 25233443 NA 2.71E-12
vg1125089512 sf1124623352 11 25089512 NA 1.27E-11
vg1124877279 sf1124411119 11 24877279 NA 4.77E-10
vg1125393477 sf1124927316 11 25393477 NA 1.36E-09
vg0716934852 sf0716933859 7 16934852 NA 2.39E-09
vg1125038070 sf1124571910 11 25038070 NA 3.44E-09
vg0328637867 sf0328630920 3 28637867 NA 6.15E-09
vg1125084128 sf1124617968 11 25084128 NA 1.03E-08
vg0704634433 sf0704633434 7 4634433 NA 1.37E-08
vg1128439104 sf1127915883 11 28439104 NA 1.44E-08
vg1125079769 sf1124613609 11 25079769 NA 2.31E-08
vg1125602304 sf1125136143 11 25602304 NA 5.44E-08
vg1125389716 sf1124923555 11 25389716 NA 7.02E-08
vg1128769420 sf1128246199 11 28769420 NA 1.14E-07
vg1122485586 sf1122019457 11 22485586 NA 1.99E-07
vg0327526494 sf0327519547 3 27526494 NA 2.02E-07