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 mr1068 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
vg0610608095 sf0610607096 6 10608095 6.77E-65 3.47E-38
vg0610872773 sf0610871774 6 10872773 2.68E-23 5.74E-14
vg0610871994 sf0610870995 6 10871994 2.32E-18 3.65E-10
vg0610419183 sf0610418184 6 10419183 3.02E-18 8.90E-19
vg0611098730 sf0611097731 6 11098730 8.19E-18 2.25E-13
vg0335408042 sf0335400911 3 35408042 2.76E-16 NA
vg0610128418 sf0610127419 6 10128418 5.24E-16 3.55E-09
vg0610016274 sf0610015275 6 10016274 1.21E-15 4.25E-12
vg0611096080 sf0611095081 6 11096080 1.50E-15 1.35E-14
vg0610419281 sf0610418282 6 10419281 8.93E-15 9.26E-09
vg0610687475 sf0610686476 6 10687475 5.52E-14 5.91E-11
vg0610488879 sf0610487880 6 10488879 1.01E-13 2.71E-08
vg0611403146 sf0611402147 6 11403146 2.53E-13 3.51E-08
vg0611999588 sf0611998589 6 11999588 4.94E-13 8.31E-08
vg0610684751 sf0610683752 6 10684751 6.40E-13 1.43E-07
vg0610752378 sf0610751379 6 10752378 3.79E-12 7.70E-12
vg0610675957 sf0610674958 6 10675957 7.22E-12 7.20E-13
vg0617815455 sf0617814458 6 17815455 2.14E-11 1.55E-08
vg0615150907 sf0615149908 6 15150907 4.70E-11 2.05E-09
vg0610449310 sf0610448311 6 10449310 9.66E-11 7.63E-09
vg0610611566 sf0610610567 6 10611566 1.37E-10 1.49E-10
vg0610556004 sf0610555005 6 10556004 6.80E-10 1.36E-08
vg0614785443 sf0614784444 6 14785443 8.29E-10 4.14E-08
vg0611643367 sf0611642368 6 11643367 7.15E-09 7.36E-08
vg0610418522 sf0610417523 6 10418522 2.02E-08 5.48E-08