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 mr1226 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
vg0719135307 sf0719134314 7 19135307 9.58E-50 1.72E-29
vg0719049906 sf0719048913 7 19049906 9.15E-46 5.71E-36
vg1101088659 sf1101087660 11 1088659 1.53E-34 NA
vg0708345272 sf0708344277 7 8345272 2.82E-34 NA
vg0504424653 sf0504424630 5 4424653 2.88E-34 NA
vg0613933042 sf0613932043 6 13933042 2.31E-33 NA
vg1101063391 sf1101062392 11 1063391 2.28E-29 NA
vg0719091461 sf0719090468 7 19091461 NA 9.00E-27
vg0719156649 sf0719155656 7 19156649 NA 1.36E-24
vg0719105731 sf0719104738 7 19105731 NA 8.46E-23
vg0719413496 sf0719412503 7 19413496 NA 1.99E-21
vg0719140498 sf0719139505 7 19140498 NA 2.06E-20
vg0719067465 sf0719066472 7 19067465 NA 3.00E-18
vg0719466615 sf0719465622 7 19466615 NA 3.45E-15
vg0707667722 sf0707666727 7 7667722 NA 2.08E-13
vg0329561125 sf0329554165 3 29561125 NA 2.33E-12
vg0719436399 sf0719435406 7 19436399 NA 1.70E-11
vg0418083292 sf0417911333 4 18083292 NA 2.82E-11
vg0718664463 sf0718663470 7 18664463 NA 4.42E-11
vg0418079489 sf0417907530 4 18079489 NA 3.09E-10
vg0909775480 sf0909774479 9 9775480 NA 1.13E-09
vg0617336375 sf0617335378 6 17336375 NA 1.64E-09
vg0421592157 sf0421420207 4 21592157 NA 1.70E-09
vg1105544417 sf1105540169 11 5544417 NA 2.95E-09
vg0625211382 sf0625210385 6 25211382 NA 3.89E-09
vg0428494128 sf0428308982 4 28494128 NA 4.45E-09
vg0719452729 sf0719451736 7 19452729 NA 5.18E-09
vg1217503545 sf1217497500 12 17503545 NA 5.85E-09
vg0720529894 sf0720528901 7 20529894 NA 1.65E-08
vg0520679043 sf0520616484 5 20679043 NA 1.98E-08
vg1103515104 sf1103511007 11 3515104 NA 2.29E-08
vg0801031318 sf0801030320 8 1031318 NA 2.30E-08