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
vg1001438303 sf1001437280 10 1438303 8.50E-43 2.80E-23
vg1016784631 sf1016713404 10 16784631 6.85E-28 NA
vg0139482357 sf0139481314 1 39482357 1.43E-27 NA
vg0130107774 sf0130106729 1 30107774 6.29E-27 4.92E-08
vg0917983991 sf0917982990 9 17983991 1.01E-26 1.66E-06
vg0922053138 sf0922052657 9 22053138 1.48E-24 2.12E-06
vg1001458161 sf1001457138 10 1458161 3.06E-24 4.83E-06
vg1002252247 sf1002251224 10 2252247 3.25E-24 1.90E-08
vg0529568293 sf0529505648 5 29568293 6.31E-24 3.06E-06
vg1001225032 sf1001224009 10 1225032 7.07E-24 2.81E-07
vg1016919266 sf1016848038 10 16919266 9.50E-24 NA
vg0918067091 sf0918066090 9 18067091 2.83E-22 9.23E-06
vg1001403288 sf1001402265 10 1403288 4.84E-22 2.01E-10
vg1001245650 sf1001244627 10 1245650 NA 7.49E-16
vg1001363789 sf1001362766 10 1363789 NA 1.90E-14
vg1001244211 sf1001243188 10 1244211 NA 2.94E-14
vg1001457313 sf1001456290 10 1457313 NA 1.84E-11
vg1002108639 sf1002107616 10 2108639 NA 2.13E-09
vg1002107770 sf1002106747 10 2107770 NA 4.08E-09
vg1001300052 sf1001299029 10 1300052 NA 2.66E-08
vg1001832131 sf1001831108 10 1832131 NA 2.56E-07
vg0818608910 sf0818606197 8 18608910 NA 3.25E-07
vg1207870021 sf1207867427 12 7870021 NA 3.92E-07
vg0422582211 sf0422397094 4 22582211 NA 4.11E-07
vg1128224267 sf1127701046 11 28224267 NA 4.19E-07
vg1000137561 sf1000136561 10 137561 NA 1.51E-06
vg0102083545 sf0102082545 1 2083545 NA 1.82E-06
vg1000290718 sf1000289718 10 290718 NA 2.42E-06
vg1000179685 sf1000178685 10 179685 NA 2.66E-06
vg0818613813 sf0818611100 8 18613813 NA 3.05E-06
vg0428715266 sf0428530117 4 28715266 NA 3.75E-06