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 mr1242 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
vg0222679274 sf0222673405 2 22679274 6.23E-53 6.61E-30
vg0222687716 sf0222681847 2 22687716 1.11E-48 9.23E-33
vg0612036184 sf0612035185 6 12036184 2.38E-28 NA
vg0304690506 sf0304689508 3 4690506 1.70E-27 NA
vg0131326153 sf0131325109 1 31326153 7.20E-27 NA
vg1223570557 sf1223537017 12 23570557 8.33E-27 NA
vg0121803138 sf0121802093 1 21803138 2.72E-25 4.18E-09
vg1110425815 sf1110420360 11 10425815 8.63E-25 1.21E-09
vg0518620627 sf0518558110 5 18620627 1.35E-24 2.43E-09
vg0221017884 sf0221012016 2 21017884 8.45E-23 NA
vg0222722554 sf0222716685 2 22722554 NA 5.12E-16
vg0141556686 sf0141555643 1 41556686 NA 4.75E-11
vg0616706040 sf0616705042 6 16706040 NA 5.62E-11
vg0141599747 sf0141598704 1 41599747 NA 1.25E-10
vg0716599841 sf0716598848 7 16599841 NA 7.28E-10
vg0222926098 sf0222920229 2 22926098 NA 8.11E-10
vg0905859096 sf0905858096 9 5859096 NA 3.07E-09
vg0626215270 sf0626214273 6 26215270 NA 3.16E-09
vg0307804640 sf0307803578 3 7804640 NA 4.72E-09
vg0327037726 sf0327030779 3 27037726 NA 4.97E-09
vg0224793205 sf0224787336 2 24793205 NA 6.11E-09
vg0316147114 sf0316145761 3 16147114 NA 9.09E-09
vg0315713125 sf0315711772 3 15713125 NA 1.07E-08
vg0222952563 sf0222946694 2 22952563 NA 1.16E-08
vg0820869390 sf0820866677 8 20869390 NA 1.46E-08
vg0709372324 sf0709371330 7 9372324 NA 1.46E-08
vg0130328652 sf0130327608 1 30328652 NA 2.86E-08
vg0431376032 sf0431190928 4 31376032 NA 2.92E-08
vg1204507349 sf1204506337 12 4507349 NA 3.79E-08
vg0311437556 sf0311436274 3 11437556 NA 7.22E-07