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 mr1609 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
vg1124970199 sf1124504039 11 24970199 2.80E-21 4.63E-11
vg1124875808 sf1124409648 11 24875808 1.75E-19 8.52E-12
vg1125048193 sf1124582033 11 25048193 1.01E-17 2.20E-07
vg1124893228 sf1124427068 11 24893228 2.65E-15 5.39E-08
vg0908878751 sf0908877750 9 8878751 2.96E-15 NA
vg0420889873 sf0420717916 4 20889873 4.18E-15 8.16E-06
vg0623252880 sf0623251883 6 23252880 4.44E-15 NA
vg0622814690 sf0622813693 6 22814690 9.94E-15 3.01E-06
vg0230509424 sf0230503555 2 30509424 4.70E-14 NA
vg1125819922 sf1125353843 11 25819922 3.25E-11 1.33E-06
vg1125432444 sf1124966283 11 25432444 4.32E-11 2.89E-06
vg1125100181 sf1124634021 11 25100181 NA 8.08E-11
vg1125022392 sf1124556232 11 25022392 NA 1.96E-09
vg1124965681 sf1124499521 11 24965681 NA 9.81E-09
vg1125037820 sf1124571660 11 25037820 NA 1.32E-08
vg1124962334 sf1124496174 11 24962334 NA 1.57E-07
vg1125009726 sf1124543566 11 25009726 NA 9.28E-07
vg1125113390 sf1124647230 11 25113390 NA 2.36E-06
vg1125915195 sf1125449114 11 25915195 NA 2.97E-06
vg1125581372 sf1125115211 11 25581372 NA 3.74E-06
vg1125118463 sf1124652303 11 25118463 NA 4.21E-06
vg0218567229 sf0218561360 2 18567229 NA 4.86E-06
vg0221203598 sf0221197730 2 21203598 NA 7.97E-06