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 2.14E-47 5.44E-21
vg1005451907 sf1005468444 10 5451907 6.39E-47 8.99E-22
vg1005371251 sf1005387788 10 5371251 2.01E-45 5.10E-21
vg1010151674 sf1010080495 10 10151674 2.13E-39 3.72E-13
vg1008389212 sf1008318074 10 8389212 3.21E-34 3.20E-15
vg1009939190 sf1009868011 10 9939190 1.27E-33 6.13E-08
vg0400368893 sf0400367892 4 368893 2.53E-33 1.07E-08
vg0203994446 sf0203994443 2 3994446 8.05E-33 5.87E-09
vg1007541835 sf1007557447 10 7541835 7.13E-32 1.05E-14
vg0231638633 sf0231632764 2 31638633 2.90E-28 4.16E-13
vg0626226028 sf0626225031 6 26226028 3.66E-28 2.44E-09
vg0306892285 sf0306891283 3 6892285 5.26E-28 5.15E-08
vg1004260807 sf1004277345 10 4260807 1.26E-27 5.40E-07
vg0235282248 sf0235276379 2 35282248 1.72E-27 8.37E-09
vg0221916521 sf0221910652 2 21916521 5.48E-27 9.62E-09
vg1005451839 sf1005468376 10 5451839 NA 3.15E-11
vg1005434563 sf1005451100 10 5434563 NA 7.64E-11
vg1120481051 sf1120014976 11 20481051 NA 4.91E-10
vg1223942507 sf1223908960 12 23942507 NA 1.51E-09
vg0812038083 sf0812037088 8 12038083 NA 3.63E-09
vg0418596045 sf0418424090 4 18596045 NA 6.11E-09
vg0202633802 sf0202633800 2 2633802 NA 8.02E-09
vg0609902526 sf0609901527 6 9902526 NA 9.60E-09
vg0325163818 sf0325161899 3 25163818 NA 1.98E-08
vg1005370191 sf1005386728 10 5370191 NA 2.58E-08
vg1008369782 sf1008298644 10 8369782 NA 3.46E-08
vg0621183896 sf0621182899 6 21183896 NA 5.22E-08
vg0626212220 sf0626211223 6 26212220 NA 8.28E-08