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 mr1090 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
vg0610566084 sf0610565085 6 10566084 9.90E-53 1.05E-47
vg0610567538 sf0610566539 6 10567538 4.77E-52 9.70E-48
vg0610567030 sf0610566031 6 10567030 5.16E-52 6.51E-48
vg0610750291 sf0610749292 6 10750291 1.56E-29 1.13E-21
vg0610547643 sf0610546644 6 10547643 7.89E-29 4.87E-23
vg0610119624 sf0610118625 6 10119624 2.61E-26 2.84E-20
vg0610684949 sf0610683950 6 10684949 5.16E-26 1.40E-16
vg0610119475 sf0610118476 6 10119475 5.85E-26 2.09E-20
vg0610681190 sf0610680191 6 10681190 4.77E-25 3.44E-25
vg0610462486 sf0610461487 6 10462486 9.80E-25 8.41E-22
vg0610679932 sf0610678933 6 10679932 6.11E-24 4.49E-25
vg0610872773 sf0610871774 6 10872773 1.09E-23 2.67E-16
vg0611098317 sf0611097318 6 11098317 7.41E-20 4.61E-17
vg0610379516 sf0610378517 6 10379516 7.99E-19 1.13E-14
vg0610435285 sf0610434286 6 10435285 3.23E-18 1.06E-21
vg0611006878 sf0611005879 6 11006878 9.61E-17 8.07E-11
vg0611292337 sf0611291338 6 11292337 5.13E-13 2.49E-13
vg0613050715 sf0613049716 6 13050715 1.42E-12 6.21E-12
vg0610211069 sf0610210070 6 10211069 9.63E-12 4.27E-12
vg0616986734 sf0616985737 6 16986734 3.13E-11 4.42E-11
vg0615150907 sf0615149908 6 15150907 4.92E-11 1.56E-09
vg0610609111 sf0610608112 6 10609111 1.08E-10 3.70E-10
vg0611654043 sf0611653044 6 11654043 3.51E-10 5.79E-11
vg0610428814 sf0610427815 6 10428814 1.36E-09 3.19E-09
vg0816239139 sf0816236425 8 16239139 4.68E-09 2.77E-09
vg0618988041 sf0618987044 6 18988041 2.49E-08 3.08E-10
vg0610272612 sf0610271613 6 10272612 8.33E-08 1.63E-08
vg0610890540 sf0610889541 6 10890540 NA 6.82E-10
vg0611628409 sf0611627410 6 11628409 NA 2.75E-09