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 mr1745 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
vg0430608671 sf0430423546 4 30608671 2.13E-19 2.29E-14
vg0430592103 sf0430406978 4 30592103 4.76E-18 2.54E-15
vg0430897454 sf0430712332 4 30897454 7.68E-11 8.96E-07
vg0308461641 sf0308460579 3 8461641 3.62E-10 2.00E-06
vg1224006854 sf1223973307 12 24006854 1.38E-09 5.11E-07
vg0430619183 sf0430434058 4 30619183 2.13E-09 3.38E-07
vg1127119606 sf1126647993 11 27119606 1.02E-08 9.21E-07
vg0225876283 sf0225870414 2 25876283 1.92E-08 1.86E-08
vg0919844661 sf0919844180 9 19844661 2.19E-07 4.21E-06
vg0602466917 sf0602465918 6 2466917 4.07E-07 3.42E-06
vg0621414627 sf0621413630 6 21414627 6.15E-07 1.16E-06
vg0427340146 sf0427155012 4 27340146 1.02E-06 1.44E-07
vg1125392589 sf1124926428 11 25392589 1.05E-06 4.37E-06
vg1216237013 sf1216234309 12 16237013 1.75E-06 1.86E-06
vg0702899416 sf0702898417 7 2899416 5.02E-06 3.35E-06
vg1125259232 sf1124793072 11 25259232 NA 1.06E-07
vg1125264457 sf1124798297 11 25264457 NA 1.94E-07
vg1125240423 sf1124774263 11 25240423 NA 1.95E-07
vg1218479048 sf1218450484 12 18479048 NA 2.54E-06