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 mr1548 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
vg1001305839 sf1001304816 10 1305839 1.06E-18 3.70E-21
vg1001381044 sf1001380021 10 1381044 3.12E-18 7.31E-22
vg1001297863 sf1001296840 10 1297863 1.48E-17 5.68E-20
vg1001271744 sf1001270721 10 1271744 1.14E-15 7.26E-17
vg1001244211 sf1001243188 10 1244211 6.55E-13 1.58E-10
vg1001434429 sf1001433406 10 1434429 5.06E-12 1.44E-14
vg1001229450 sf1001228427 10 1229450 5.22E-12 1.91E-15
vg1001306734 sf1001305711 10 1306734 1.85E-10 1.25E-09
vg1001367351 sf1001366328 10 1367351 1.92E-09 1.09E-07
vg1001498051 sf1001497028 10 1498051 7.75E-09 6.64E-10
vg0713015489 sf0713014496 7 13015489 1.64E-08 2.76E-07
vg0707891668 sf0707890673 7 7891668 1.70E-08 1.61E-08
vg1001438740 sf1001437717 10 1438740 2.35E-08 1.47E-09
vg0412555488 sf0412546198 4 12555488 3.85E-07 8.91E-07
vg0919514800 sf0919514390 9 19514800 4.23E-07 1.61E-06
vg0227043009 sf0227037140 2 27043009 6.36E-07 1.31E-06
vg0818608910 sf0818606197 8 18608910 8.16E-07 2.14E-07
vg0235591964 sf0235586095 2 35591964 4.91E-06 9.26E-07
vg1002108639 sf1002107616 10 2108639 5.87E-06 3.16E-08
vg0226200932 sf0226195063 2 26200932 6.93E-06 8.29E-07
vg1203735229 sf1203734228 12 3735229 7.33E-06 6.22E-07
vg1023072166 sf1023000639 10 23072166 NA 4.08E-07
vg1005841875 sf1005858413 10 5841875 NA 1.02E-06
vg0529568293 sf0529505648 5 29568293 NA 1.65E-06