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 mr1310 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
vg1000442554 sf1000441530 10 442554 1.13E-85 1.71E-49
vg1000576410 sf1000575386 10 576410 5.64E-85 4.08E-50
vg1011122210 sf1011051030 10 11122210 8.56E-41 8.49E-09
vg1008207053 sf1008135915 10 8207053 4.02E-39 2.73E-10
vg0408443712 sf0408438986 4 8443712 5.68E-39 5.96E-07
vg0516197972 sf0516140454 5 16197972 6.15E-38 2.17E-06
vg0528039299 sf0527976654 5 28039299 9.87E-34 1.44E-11
vg0330834913 sf0330827800 3 30834913 2.96E-33 4.23E-12
vg0327762028 sf0327755081 3 27762028 2.34E-32 3.93E-10
vg1125100181 sf1124634021 11 25100181 6.98E-32 1.55E-10
vg1125037120 sf1124570960 11 25037120 NA 3.70E-19
vg1125115838 sf1124649678 11 25115838 NA 4.42E-14
vg1000493003 sf1000491979 10 493003 NA 5.57E-13
vg0327915031 sf0327908085 3 27915031 NA 5.68E-13
vg1000736230 sf1000735206 10 736230 NA 2.31E-12
vg1001500479 sf1001499456 10 1500479 NA 5.89E-11
vg1000551614 sf1000550590 10 551614 NA 1.89E-10
vg1000604594 sf1000603570 10 604594 NA 3.47E-10
vg1000572925 sf1000571901 10 572925 NA 3.69E-10
vg1000740409 sf1000739385 10 740409 NA 4.20E-10
vg1000770027 sf1000769003 10 770027 NA 4.96E-10
vg0607242294 sf0607241295 6 7242294 NA 7.61E-10
vg1000661364 sf1000660340 10 661364 NA 8.71E-10
vg1000741800 sf1000740776 10 741800 NA 9.35E-10
vg1128846586 sf1128323365 11 28846586 NA 1.47E-09
vg1000647605 sf1000646581 10 647605 NA 1.56E-09
vg1000231687 sf1000230687 10 231687 NA 2.92E-09
vg1214644112 sf1214641452 12 14644112 NA 4.80E-09
vg1000647302 sf1000646278 10 647302 NA 5.04E-09
vg1000538898 sf1000537874 10 538898 NA 5.94E-09
vg1000646061 sf1000645037 10 646061 NA 6.88E-09