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 mr1079 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
vg1215968758 sf1215966054 12 15968758 4.19E-80 3.72E-34
vg1215854982 sf1215852278 12 15854982 8.31E-75 2.52E-34
vg1209571445 sf1209568854 12 9571445 5.55E-59 1.15E-21
vg1210300519 sf1210297932 12 10300519 1.13E-55 2.16E-26
vg1223872806 sf1223839259 12 23872806 2.57E-46 3.06E-09
vg1223898220 sf1223864673 12 23898220 1.71E-40 1.99E-10
vg1212726422 sf1212723761 12 12726422 8.48E-29 2.74E-07
vg1212938220 sf1212935559 12 12938220 1.46E-27 3.00E-07
vg1219911712 sf1219883182 12 19911712 6.54E-25 NA
vg1207616892 sf1207614298 12 7616892 8.83E-22 1.61E-06
vg1017847198 sf1017775971 10 17847198 3.08E-21 9.98E-07
vg0217462843 sf0217456973 2 17462843 4.73E-19 2.08E-07
vg1209926499 sf1209923909 12 9926499 9.36E-19 1.56E-06
vg0526374490 sf0526311853 5 26374490 3.14E-17 1.33E-06
vg1215956521 sf1215953817 12 15956521 1.41E-16 1.27E-08
vg1216192039 sf1216189335 12 16192039 1.43E-16 3.41E-13
vg1216680196 sf1216674150 12 16680196 2.10E-16 1.23E-06
vg1215983666 sf1215980962 12 15983666 1.14E-15 1.40E-06
vg1207570300 sf1207567705 12 7570300 3.67E-13 4.57E-11
vg1210429306 sf1210426719 12 10429306 5.02E-13 1.92E-06
vg1215976836 sf1215974132 12 15976836 1.08E-12 1.16E-06
vg1214706284 sf1214703625 12 14706284 1.25E-12 4.70E-07
vg1114869295 sf1114405609 11 14869295 NA 4.77E-08
vg0319910078 sf0319908589 3 19910078 NA 5.39E-07
vg0404944968 sf0404940407 4 4944968 NA 1.65E-06