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 mr1238 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 3.79E-72 7.35E-54
vg1125079736 sf1124613576 11 25079736 3.65E-33 1.56E-31
vg1125432444 sf1124966283 11 25432444 3.70E-33 1.79E-14
vg0704627367 sf0704626368 7 4627367 2.58E-32 1.39E-09
vg1122647736 sf1122181607 11 22647736 7.01E-32 1.10E-07
vg0619650349 sf0619649352 6 19650349 1.78E-31 7.87E-07
vg1124989620 sf1124523460 11 24989620 4.35E-29 3.33E-23
vg1124875808 sf1124409648 11 24875808 1.18E-27 6.36E-15
vg1124966740 sf1124500580 11 24966740 1.32E-27 9.97E-25
vg1124989458 sf1124523298 11 24989458 NA 1.28E-24
vg1125233443 sf1124767283 11 25233443 NA 1.65E-18
vg1125120298 sf1124654138 11 25120298 NA 2.63E-18
vg1125089512 sf1124623352 11 25089512 NA 5.74E-17
vg1125080303 sf1124614143 11 25080303 NA 1.05E-15
vg1124988847 sf1124522687 11 24988847 NA 1.39E-15
vg1125390548 sf1124924387 11 25390548 NA 1.75E-15
vg1125257504 sf1124791344 11 25257504 NA 1.05E-10
vg1125600946 sf1125134785 11 25600946 NA 1.50E-10
vg0716934852 sf0716933859 7 16934852 NA 2.44E-10
vg1125091275 sf1124625115 11 25091275 NA 2.58E-10
vg1125079888 sf1124613728 11 25079888 NA 3.12E-10
vg1124256871 sf1123790741 11 24256871 NA 1.01E-09
vg1125063819 sf1124597659 11 25063819 NA 1.88E-09
vg1122487739 sf1122021610 11 22487739 NA 3.32E-09
vg1125389716 sf1124923555 11 25389716 NA 4.36E-09
vg1125534637 sf1125068476 11 25534637 NA 1.46E-08
vg0307571121 sf0307570059 3 7571121 NA 1.93E-08
vg1008205727 sf1008134589 10 8205727 NA 2.52E-07
vg0812798675 sf0812796500 8 12798675 NA 4.30E-06