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 mr1676 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
vg0920049900 sf0920049419 9 20049900 6.08E-34 4.64E-07
vg0920359641 sf0920359160 9 20359641 4.65E-30 2.63E-09
vg0920166366 sf0920165885 9 20166366 1.99E-28 5.28E-11
vg0107011488 sf0107010488 1 7011488 6.13E-27 5.44E-11
vg0106989975 sf0106988975 1 6989975 8.79E-27 2.90E-11
vg0917493382 sf0917492381 9 17493382 9.99E-26 NA
vg0618007086 sf0618006089 6 18007086 1.01E-25 NA
vg0305233552 sf0305232552 3 5233552 3.62E-25 3.70E-07
vg0806496391 sf0806495396 8 6496391 6.24E-23 7.25E-07
vg0401219405 sf0401214955 4 1219405 1.00E-21 NA
vg0817460370 sf0817457656 8 17460370 2.79E-21 2.79E-07
vg0311016054 sf0311014772 3 11016054 7.67E-20 4.36E-06
vg0107015621 sf0107014621 1 7015621 NA 2.51E-12
vg0107032630 sf0107031630 1 7032630 NA 5.03E-09
vg1221475948 sf1221442495 12 21475948 NA 2.64E-08
vg0129279095 sf0129278050 1 29279095 NA 6.75E-07
vg1114401329 sf1113937646 11 14401329 NA 7.56E-07
vg1114401699 sf1113938016 11 14401699 NA 8.33E-07
vg0825549651 sf0825546937 8 25549651 NA 8.69E-07
vg0809379318 sf0809378322 8 9379318 NA 2.06E-06
vg1211536265 sf1211533601 12 11536265 NA 2.74E-06
vg0212094045 sf0212094041 2 12094045 NA 2.84E-06
vg0208025341 sf0208025340 2 8025341 NA 4.49E-06
vg0127041564 sf0127040520 1 27041564 NA 4.74E-06
vg0208608994 sf0208608993 2 8608994 NA 4.92E-06