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 mr1093 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
vg0216752678 sf0216746808 2 16752678 6.49E-27 3.54E-17
vg0217047369 sf0217041499 2 17047369 1.70E-26 7.33E-18
vg0217539704 sf0217533834 2 17539704 1.80E-19 7.03E-09
vg0216888886 sf0216883016 2 16888886 7.02E-18 4.26E-09
vg1210426367 sf1210423780 12 10426367 3.00E-16 9.78E-06
vg1210412113 sf1210409526 12 10412113 5.49E-16 5.68E-07
vg1217425791 sf1217419746 12 17425791 2.17E-15 NA
vg0220408553 sf0220402685 2 20408553 1.67E-14 NA
vg0216134521 sf0216128651 2 16134521 3.26E-14 3.97E-07
vg0213525745 sf0213525741 2 13525745 1.63E-13 8.68E-07
vg0216666509 sf0216660639 2 16666509 5.30E-13 1.12E-06
vg1217366858 sf1217360813 12 17366858 6.80E-13 4.43E-06
vg0218852605 sf0218846736 2 18852605 9.45E-13 1.46E-07
vg0217737734 sf0217731864 2 17737734 5.19E-12 5.24E-07
vg0217709534 sf0217703664 2 17709534 5.42E-09 2.68E-06
vg0919309710 sf0919309300 9 19309710 2.05E-08 NA
vg0411806765 sf0411797476 4 11806765 6.93E-08 1.50E-07
vg0116760985 sf0116759959 1 16760985 NA 2.94E-07
vg0525571166 sf0525508587 5 25571166 NA 3.87E-07
vg0618947595 sf0618946598 6 18947595 NA 7.20E-07
vg0216876069 sf0216870199 2 16876069 NA 2.59E-06