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 mr1392 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
vg0916428508 sf0916427507 9 16428508 8.36E-10 NA
vg0420166000 sf0419994038 4 20166000 3.54E-09 1.90E-07
vg0208739949 sf0208739948 2 8739949 3.59E-09 NA
vg1002045263 sf1002044240 10 2045263 4.09E-09 NA
vg0618125425 sf0618124428 6 18125425 4.70E-09 NA
vg0302287012 sf0302286008 3 2287012 5.23E-09 NA
vg0420165708 sf0419993746 4 20165708 2.05E-08 2.12E-06
vg1215653812 sf1215651109 12 15653812 3.54E-08 2.27E-06
vg0130154178 sf0130153133 1 30154178 5.29E-08 3.85E-06
vg0208312505 sf0208312504 2 8312505 7.58E-08 1.25E-06
vg0406783001 sf0406778446 4 6783001 1.29E-07 4.18E-06
vg0434845632 sf0434660523 4 34845632 5.36E-07 4.11E-06
vg0130967803 sf0130966759 1 30967803 5.73E-07 2.44E-06
vg0226270478 sf0226264609 2 26270478 5.91E-07 NA
vg1109375967 sf1109370544 11 9375967 5.93E-07 2.45E-06
vg1021305364 sf1021233842 10 21305364 6.27E-07 4.19E-06
vg0527177036 sf0527114392 5 27177036 7.71E-07 2.45E-06
vg0224428620 sf0224422751 2 24428620 1.09E-06 3.80E-06
vg0131435897 sf0131434853 1 31435897 1.30E-06 6.08E-06
vg0207218977 sf0207218977 2 7218977 1.81E-06 NA
vg1212799792 sf1212797131 12 12799792 NA 2.61E-08
vg0409860484 sf0409851182 4 9860484 NA 9.98E-08
vg1210659716 sf1210657129 12 10659716 NA 8.58E-07
vg0409861872 sf0409852570 4 9861872 NA 8.89E-07
vg0603482934 sf0603481935 6 3482934 NA 1.49E-06
vg0402244708 sf0402240303 4 2244708 NA 2.44E-06