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 mr1134 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
vg0137930974 sf0137929931 1 37930974 6.51E-21 5.46E-17
vg0811356623 sf0811355628 8 11356623 2.81E-09 NA
vg0221380177 sf0221374309 2 21380177 5.81E-09 1.85E-07
vg0108147243 sf0108146243 1 8147243 1.84E-08 2.82E-07
vg0812030698 sf0812029703 8 12030698 1.97E-08 1.11E-06
vg0317222323 sf0317221133 3 17222323 4.44E-08 NA
vg0712987215 sf0712986222 7 12987215 4.75E-08 1.12E-07
vg0405835279 sf0405830718 4 5835279 1.04E-07 1.12E-06
vg1123450985 sf1122984855 11 23450985 1.72E-07 6.38E-07
vg0810040454 sf0810039458 8 10040454 1.73E-07 6.82E-07
vg0425798257 sf0425613121 4 25798257 2.30E-07 5.20E-08
vg0812028320 sf0812027325 8 12028320 8.67E-07 NA
vg0714431042 sf0714430049 7 14431042 9.95E-07 2.08E-06
vg0910545581 sf0910544580 9 10545581 1.56E-06 8.06E-07
vg0121412555 sf0121411510 1 21412555 2.28E-06 1.05E-06
vg1125171325 sf1124705165 11 25171325 2.50E-06 5.04E-07
vg1212596614 sf1212593953 12 12596614 2.55E-06 8.53E-07
vg1217955288 sf1217926723 12 17955288 4.44E-06 1.45E-06
vg0406527932 sf0406523375 4 6527932 6.67E-06 1.86E-06
vg1017593628 sf1017522401 10 17593628 7.34E-06 2.52E-06
vg0406043021 sf0406038460 4 6043021 NA 5.39E-07
vg1017843487 sf1017772260 10 17843487 NA 1.83E-06
vg1206249313 sf1206248203 12 6249313 NA 2.39E-06