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 mr1082 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
vg0719067465 sf0719066472 7 19067465 2.41E-28 9.49E-21
vg0719006525 sf0719005532 7 19006525 2.59E-28 8.71E-21
vg0719025599 sf0719024606 7 19025599 1.39E-14 1.23E-09
vg1101911438 sf1101910439 11 1911438 2.42E-12 4.66E-09
vg0804032788 sf0804031791 8 4032788 1.56E-11 9.26E-07
vg0700416280 sf0700415280 7 416280 1.94E-11 3.28E-07
vg0422855440 sf0422670325 4 22855440 2.15E-11 2.45E-08
vg0421351123 sf0421179177 4 21351123 3.76E-11 2.50E-07
vg0408294186 sf0408289460 4 8294186 4.58E-11 2.13E-06
vg0309326904 sf0309325840 3 9326904 8.50E-11 1.86E-06
vg0705107520 sf0705106521 7 5107520 2.11E-10 7.59E-10
vg0124676757 sf0124675713 1 24676757 3.19E-10 6.15E-08
vg0417551912 sf0417379954 4 17551912 4.31E-10 2.43E-07
vg0112831041 sf0112830015 1 12831041 6.49E-10 3.64E-08
vg0130667376 sf0130666332 1 30667376 8.73E-10 5.95E-07
vg0816207802 sf0816205088 8 16207802 1.22E-09 1.13E-07
vg0401764682 sf0401760281 4 1764682 4.64E-09 1.90E-06
vg0627547379 sf0627546381 6 27547379 2.09E-08 1.62E-06
vg0709019375 sf0709018381 7 9019375 3.59E-08 5.54E-07
vg0622463338 sf0622462341 6 22463338 7.84E-07 2.01E-06
vg0719056561 sf0719055568 7 19056561 2.22E-06 9.88E-14
vg1118755597 sf1118289405 11 18755597 5.91E-06 3.31E-07
vg0719199004 sf0719198011 7 19199004 NA 8.80E-12
vg0435372935 sf0435187817 4 35372935 NA 1.74E-06