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 mr1139 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
vg0719007567 sf0719006574 7 19007567 1.32E-22 1.37E-18
vg0717227488 sf0717226495 7 17227488 4.27E-14 1.95E-10
vg0719140489 sf0719139496 7 19140489 1.50E-12 3.86E-08
vg1201736678 sf1201735676 12 1736678 9.25E-12 1.06E-07
vg0323471529 sf0323469703 3 23471529 7.30E-11 1.15E-06
vg0431282979 sf0431097869 4 31282979 1.49E-10 2.36E-06
vg0718862824 sf0718861831 7 18862824 3.41E-08 1.58E-06
vg1201535349 sf1201534349 12 1535349 7.74E-08 3.81E-06
vg0718985745 sf0718984752 7 18985745 2.29E-07 4.09E-09
vg0611537645 sf0611536646 6 11537645 2.43E-07 8.92E-07
vg0314683577 sf0314682264 3 14683577 6.25E-07 NA
vg1206187052 sf1206185943 12 6187052 9.50E-07 4.56E-06
vg0719143007 sf0719142014 7 19143007 1.02E-06 1.18E-06
vg0717285474 sf0717284481 7 17285474 2.16E-06 2.12E-07
vg1009450763 sf1009379584 10 9450763 4.76E-06 1.11E-06
vg1121617620 sf1121151497 11 21617620 7.04E-06 6.59E-06
vg0719484643 sf0719483650 7 19484643 NA 1.44E-07
vg1111310432 sf1111304749 11 11310432 NA 1.12E-06
vg0228211407 sf0228205538 2 28211407 NA 2.93E-06
vg1007460883 sf1007476506 10 7460883 NA 3.37E-06
vg0826160404 sf0826157690 8 26160404 NA 4.45E-06