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 mr1395 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
vg0406393570 sf0406389010 4 6393570 2.26E-133 2.05E-26
vg0406519287 sf0406514730 4 6519287 7.43E-127 1.57E-24
vg1017440840 sf1017369613 10 17440840 4.68E-103 1.92E-07
vg0305431587 sf0305430587 3 5431587 4.16E-102 NA
vg0411344776 sf0411335479 4 11344776 8.86E-102 NA
vg0718812067 sf0718811074 7 18812067 2.43E-100 NA
vg0613777657 sf0613776658 6 13777657 3.92E-94 1.88E-09
vg0711094601 sf0711093607 7 11094601 3.58E-92 1.64E-07
vg0916689948 sf0916688947 9 16689948 1.41E-91 1.02E-06
vg0406488042 sf0406483485 4 6488042 NA 1.35E-10
vg0619719272 sf0619718275 6 19719272 NA 4.15E-10
vg0406345405 sf0406340845 4 6345405 NA 1.13E-07
vg0715849539 sf0715848546 7 15849539 NA 1.37E-07
vg1209907443 sf1209904853 12 9907443 NA 2.13E-07
vg1017923788 sf1017852560 10 17923788 NA 2.91E-07
vg0406489536 sf0406484979 4 6489536 NA 3.62E-07
vg0806593377 sf0806592382 8 6593377 NA 7.10E-07
vg0520441815 sf0520379286 5 20441815 NA 9.38E-07
vg0706562154 sf0706561159 7 6562154 NA 1.05E-06
vg0124267851 sf0124266807 1 24267851 NA 1.23E-06
vg1123064286 sf1122598157 11 23064286 NA 1.84E-06
vg0415203123 sf0415193838 4 15203123 NA 2.20E-06
vg1209714251 sf1209711660 12 9714251 NA 2.43E-06
vg0720714007 sf0720713014 7 20714007 NA 3.14E-06
vg0722680756 sf0722679763 7 22680756 NA 3.45E-06
vg0906865440 sf0906864440 9 6865440 NA 3.61E-06
vg0717100285 sf0717099292 7 17100285 NA 8.69E-06