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 mr1705 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
vg0716391496 sf0716390503 7 16391496 8.42E-19 1.79E-09
vg0716335933 sf0716334940 7 16335933 1.93E-16 2.87E-07
vg0629905605 sf0629904607 6 29905605 2.22E-16 NA
vg0716393936 sf0716392943 7 16393936 7.36E-16 7.48E-07
vg0716355931 sf0716354938 7 16355931 3.60E-15 6.15E-07
vg0825471248 sf0825468534 8 25471248 3.38E-14 NA
vg0115383222 sf0115382196 1 15383222 6.28E-10 NA
vg0117282717 sf0117281671 1 17282717 1.31E-09 4.91E-06
vg0716554289 sf0716553296 7 16554289 NA 1.62E-07
vg0205395417 sf0205395417 2 5395417 NA 3.67E-07
vg1217606407 sf1217600362 12 17606407 NA 4.63E-07
vg0909371011 sf0909370010 9 9371011 NA 5.17E-07
vg0502285091 sf0502285066 5 2285091 NA 8.29E-07
vg1105884811 sf1105880563 11 5884811 NA 1.36E-06
vg0107778488 sf0107777488 1 7778488 NA 1.57E-06
vg0336059101 sf0336051970 3 36059101 NA 1.64E-06
vg0716445309 sf0716444316 7 16445309 NA 1.83E-06
vg1216315099 sf1216312395 12 16315099 NA 2.10E-06
vg1106255697 sf1106251449 11 6255697 NA 3.03E-06
vg0324941311 sf0324939391 3 24941311 NA 4.02E-06
vg0205621590 sf0205621590 2 5621590 NA 4.83E-06
vg0107903346 sf0107902346 1 7903346 NA 4.97E-06
vg0413048245 sf0413038955 4 13048245 NA 8.37E-06
vg0815304114 sf0815301400 8 15304114 NA 9.68E-06