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 mr1599 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
vg0216752678 sf0216746808 2 16752678 1.20E-38 5.05E-24
vg0217047369 sf0217041499 2 17047369 3.60E-38 3.61E-25
vg0213525745 sf0213525741 2 13525745 2.04E-19 2.16E-09
vg0217739410 sf0217733540 2 17739410 4.32E-18 6.14E-11
vg0216476829 sf0216470959 2 16476829 8.29E-18 1.48E-08
vg0216372724 sf0216366854 2 16372724 1.61E-16 7.05E-09
vg1210519897 sf1210517310 12 10519897 2.51E-16 NA
vg1210467503 sf1210464916 12 10467503 5.30E-16 1.36E-07
vg1210451520 sf1210448933 12 10451520 2.03E-15 5.98E-07
vg1217578105 sf1217572060 12 17578105 2.39E-15 NA
vg0216666516 sf0216660646 2 16666516 6.75E-15 7.15E-09
vg1217440211 sf1217434166 12 17440211 1.03E-14 4.64E-06
vg0217377905 sf0217372035 2 17377905 1.05E-14 2.78E-06
vg0217654127 sf0217648257 2 17654127 5.07E-14 8.67E-07
vg0217737734 sf0217731864 2 17737734 2.08E-13 1.61E-08
vg0216888886 sf0216883016 2 16888886 5.27E-13 4.15E-06
vg0900336799 sf0900335799 9 336799 1.26E-12 3.00E-06
vg0216278300 sf0216272430 2 16278300 1.80E-12 1.08E-06
vg1005364262 sf1005380799 10 5364262 3.50E-08 1.11E-06
vg0216876069 sf0216870199 2 16876069 NA 2.98E-08
vg0526012382 sf0525949802 5 26012382 NA 4.18E-08
vg0525534836 sf0525472257 5 25534836 NA 8.85E-08
vg0116760985 sf0116759959 1 16760985 NA 5.53E-07
vg0411806765 sf0411797476 4 11806765 NA 1.25E-06
vg0514184495 sf0514127039 5 14184495 NA 3.13E-06