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 mr1409 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
vg1008639326 sf1008568188 10 8639326 2.16E-20 NA
vg1005435328 sf1005451865 10 5435328 5.90E-20 6.07E-07
vg1005436815 sf1005453352 10 5436815 9.95E-20 5.83E-07
vg0423066481 sf0422881336 4 23066481 2.22E-18 NA
vg1021243184 sf1021171662 10 21243184 1.04E-17 NA
vg1226454359 sf1226420753 12 26454359 3.23E-17 NA
vg0335000939 sf0334993809 3 35000939 1.65E-14 1.56E-07
vg0216756407 sf0216750537 2 16756407 2.40E-12 7.72E-08
vg0433346651 sf0433161541 4 33346651 4.71E-12 NA
vg0327447631 sf0327440684 3 27447631 NA 1.27E-07
vg0327425445 sf0327418498 3 27425445 NA 2.14E-07
vg0202722002 sf0202722000 2 2722002 NA 4.52E-07
vg0317023117 sf0317021991 3 17023117 NA 5.07E-07
vg0202699054 sf0202699052 2 2699054 NA 5.98E-07
vg0202725085 sf0202725083 2 2725085 NA 6.91E-07
vg0307980063 sf0307979001 3 7980063 NA 8.66E-07
vg0628001136 sf0628000138 6 28001136 NA 9.50E-07
vg1103105609 sf1103101512 11 3105609 NA 1.14E-06
vg0401213700 sf0401209250 4 1213700 NA 1.20E-06
vg0216629891 sf0216624021 2 16629891 NA 1.27E-06
vg0324795678 sf0324793757 3 24795678 NA 1.30E-06
vg0631103106 sf0631102108 6 31103106 NA 2.14E-06
vg1110517362 sf1110511907 11 10517362 NA 2.57E-06
vg1121561200 sf1121095077 11 21561200 NA 2.87E-06