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 mr1619 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
vg0222746228 sf0222740359 2 22746228 1.07E-19 6.11E-10
vg0222752774 sf0222746905 2 22752774 4.00E-17 7.47E-11
vg0406948268 sf0406943536 4 6948268 1.13E-14 5.42E-08
vg0205358849 sf0205358849 2 5358849 2.37E-13 5.57E-06
vg0406944478 sf0406939746 4 6944478 1.25E-12 1.67E-08
vg0224620629 sf0224614760 2 24620629 1.65E-11 NA
vg0120435894 sf0120434849 1 20435894 3.38E-11 NA
vg0406620026 sf0406615470 4 6620026 1.43E-10 2.00E-06
vg1107318404 sf1107314149 11 7318404 2.56E-09 1.87E-06
vg0411627027 sf0411617731 4 11627027 2.99E-09 6.91E-07
vg0618618072 sf0618617075 6 18618072 3.34E-09 1.81E-08
vg0205562421 sf0205562421 2 5562421 4.00E-09 2.02E-06
vg0613439992 sf0613438993 6 13439992 8.98E-09 3.53E-07
vg0419961351 sf0419789387 4 19961351 1.68E-08 3.72E-07
vg1216930362 sf1216924316 12 16930362 4.63E-08 4.97E-08
vg0507926447 sf0507926388 5 7926447 5.36E-08 1.20E-06
vg0708285419 sf0708284424 7 8285419 5.86E-08 NA
vg0403617354 sf0403612957 4 3617354 6.22E-08 8.49E-07
vg0122178298 sf0122177253 1 22178298 1.48E-07 NA
vg0806502338 sf0806501343 8 6502338 5.56E-07 6.87E-07
vg0507863180 sf0507863121 5 7863180 6.29E-07 NA
vg0412144728 sf0412135439 4 12144728 7.84E-07 1.36E-06
vg0411431095 sf0411421797 4 11431095 9.47E-07 1.90E-06
vg0222589023 sf0222583154 2 22589023 NA 3.21E-07
vg1215976459 sf1215973755 12 15976459 NA 5.52E-07
vg0407872167 sf0407867435 4 7872167 NA 9.61E-07
vg0525534836 sf0525472257 5 25534836 NA 1.75E-06
vg0406877319 sf0406872764 4 6877319 NA 1.90E-06
vg0911368113 sf0911367112 9 11368113 NA 4.39E-06