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 mr1962 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
vg0406465683 sf0406461126 4 6465683 1.45E-36 2.07E-25
vg0406170395 sf0406165835 4 6170395 8.89E-21 6.33E-12
vg0817327521 sf0817324807 8 17327521 7.66E-15 1.25E-09
vg0807357132 sf0807356137 8 7357132 1.43E-13 5.62E-10
vg0405052013 sf0405047452 4 5052013 1.35E-11 1.05E-07
vg0406056639 sf0406052078 4 6056639 1.30E-10 5.68E-08
vg0503312521 sf0503312497 5 3312521 5.73E-10 9.74E-07
vg0143110708 sf0143109664 1 43110708 3.00E-08 4.72E-07
vg1222372938 sf1222339377 12 22372938 5.85E-08 2.64E-06
vg1116629534 sf1116164412 11 16629534 9.08E-07 4.48E-07
vg0307373114 sf0307372112 3 7373114 2.93E-06 2.59E-06
vg1227091155 sf1227057554 12 27091155 4.93E-06 9.63E-09
vg1129006509 sf1128483288 11 29006509 NA 3.32E-07
vg0313206866 sf0313205584 3 13206866 NA 3.79E-07
vg1223855861 sf1223822314 12 23855861 NA 4.06E-07
vg0509425592 sf0509425521 5 9425592 NA 4.96E-07
vg0707026528 sf0707025533 7 7026528 NA 7.33E-07
vg0233693401 sf0233687532 2 33693401 NA 9.17E-07
vg0626331514 sf0626330517 6 26331514 NA 1.65E-06
vg0133680937 sf0133679893 1 33680937 NA 2.01E-06
vg0203590903 sf0203590900 2 3590903 NA 2.40E-06