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 mr1768 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
vg1005366897 sf1005383434 10 5366897 6.37E-29 1.00E-14
vg1005451907 sf1005468444 10 5451907 4.98E-28 8.72E-15
vg1005371251 sf1005387788 10 5371251 5.26E-27 6.37E-14
vg1009165657 sf1009094478 10 9165657 5.25E-25 1.03E-09
vg1009899148 sf1009827969 10 9899148 2.18E-24 2.91E-11
vg1002961240 sf1002960217 10 2961240 9.28E-23 1.44E-08
vg1002866098 sf1002865075 10 2866098 2.03E-22 1.88E-07
vg1010268867 sf1010197688 10 10268867 4.27E-22 4.94E-11
vg0719634338 sf0719633345 7 19634338 8.98E-22 3.16E-07
vg0420877857 sf0420705900 4 20877857 1.30E-21 2.28E-07
vg0815176909 sf0815174195 8 15176909 9.59E-21 1.20E-06
vg1004260807 sf1004277345 10 4260807 9.67E-21 2.53E-09
vg1105575325 sf1105571077 11 5575325 1.85E-19 4.03E-07
vg0114073794 sf0114072768 1 14073794 1.96E-19 4.88E-07
vg0626226028 sf0626225031 6 26226028 1.01E-18 1.26E-06
vg0824322535 sf0824319821 8 24322535 2.69E-18 5.02E-07
vg0420837856 sf0420665899 4 20837856 3.13E-18 3.15E-08
vg0231638633 sf0231632764 2 31638633 8.23E-17 1.17E-07
vg1004738097 sf1004754634 10 4738097 NA 2.99E-08
vg0503172777 sf0503172753 5 3172777 NA 1.12E-07
vg0420788121 sf0420616164 4 20788121 NA 1.73E-07
vg1114265238 sf1113801559 11 14265238 NA 6.46E-07
vg1007270757 sf1007286380 10 7270757 NA 7.19E-07
vg0828077780 sf0828075066 8 28077780 NA 7.98E-07
vg1005630402 sf1005646940 10 5630402 NA 8.70E-07
vg0706460655 sf0706459660 7 6460655 NA 9.86E-07
vg0220187125 sf0220181257 2 20187125 NA 1.13E-06
vg1005356435 sf1005372972 10 5356435 NA 1.23E-06