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 mr1495 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
vg1009096302 sf1009025163 10 9096302 3.22E-44 5.57E-08
vg0222727801 sf0222721932 2 22727801 1.79E-40 3.54E-11
vg0222719604 sf0222713735 2 22719604 3.17E-40 1.85E-11
vg0222743508 sf0222737639 2 22743508 4.69E-39 4.08E-10
vg1006502151 sf1006517774 10 6502151 6.55E-39 3.68E-06
vg1009141969 sf1009070830 10 9141969 1.86E-32 7.47E-08
vg1009172946 sf1009101767 10 9172946 2.57E-31 1.51E-08
vg1001393119 sf1001392096 10 1393119 1.74E-30 NA
vg0222889740 sf0222883871 2 22889740 4.21E-30 1.37E-17
vg1005491113 sf1005507650 10 5491113 8.46E-28 3.04E-08
vg0222693356 sf0222687487 2 22693356 1.05E-27 4.42E-17
vg1008708441 sf1008637303 10 8708441 2.00E-27 6.09E-11
vg1002973972 sf1002972949 10 2973972 7.26E-27 8.96E-07
vg1216843191 sf1216837145 12 16843191 7.37E-24 2.15E-09
vg1007427631 sf1007443254 10 7427631 NA 2.83E-14
vg1006839627 sf1006855250 10 6839627 NA 8.68E-14
vg1009127352 sf1009056213 10 9127352 NA 2.46E-11
vg1008992008 sf1008920869 10 8992008 NA 2.49E-09
vg0222570184 sf0222564315 2 22570184 NA 8.41E-09
vg0141558120 sf0141557077 1 41558120 NA 8.93E-09
vg0407826743 sf0407822011 4 7826743 NA 1.50E-08
vg0434765473 sf0434580364 4 34765473 NA 5.35E-08
vg1005654495 sf1005671033 10 5654495 NA 9.25E-08
vg0104923119 sf0104922119 1 4923119 NA 2.17E-07
vg1008978200 sf1008907061 10 8978200 NA 2.43E-07
vg0825885835 sf0825883121 8 25885835 NA 3.26E-07
vg0822460634 sf0822457921 8 22460634 NA 3.45E-07
vg0721144668 sf0721143675 7 21144668 NA 6.66E-07
vg0624490434 sf0624489437 6 24490434 NA 7.70E-07
vg1110107248 sf1110101825 11 10107248 NA 9.20E-07