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 mr1841 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
vg1125118463 sf1124652303 11 25118463 1.29E-40 8.43E-31
vg1124958705 sf1124492545 11 24958705 4.88E-31 5.80E-09
vg1125063819 sf1124597659 11 25063819 1.38E-28 5.89E-09
vg0812486826 sf0812485730 8 12486826 2.24E-28 5.64E-06
vg0822138203 sf0822135490 8 22138203 3.64E-28 NA
vg1124875808 sf1124409648 11 24875808 4.17E-28 9.33E-16
vg0333794340 sf0333787210 3 33794340 1.23E-27 NA
vg1124989458 sf1124523298 11 24989458 2.04E-25 2.16E-21
vg1009498741 sf1009427562 10 9498741 7.75E-23 NA
vg1124986792 sf1124520632 11 24986792 NA 2.29E-19
vg1125113622 sf1124647462 11 25113622 NA 2.57E-16
vg1125113390 sf1124647230 11 25113390 NA 3.74E-12
vg1125080303 sf1124614143 11 25080303 NA 8.47E-12
vg1125085953 sf1124619793 11 25085953 NA 1.18E-11
vg1124988728 sf1124522568 11 24988728 NA 4.27E-11
vg1125393477 sf1124927316 11 25393477 NA 1.51E-10
vg1125081311 sf1124615151 11 25081311 NA 1.95E-10
vg1125089276 sf1124623116 11 25089276 NA 3.78E-10
vg0224638374 sf0224632505 2 24638374 NA 1.70E-08
vg1124877279 sf1124411119 11 24877279 NA 3.30E-08
vg1125084815 sf1124618655 11 25084815 NA 1.08E-07
vg0716934852 sf0716933859 7 16934852 NA 1.17E-07
vg1124348408 sf1123882252 11 24348408 NA 1.24E-07
vg1125602304 sf1125136143 11 25602304 NA 1.30E-07
vg1124975731 sf1124509571 11 24975731 NA 1.70E-07
vg0812148045 sf0812147050 8 12148045 NA 1.71E-07
vg1125389716 sf1124923555 11 25389716 NA 1.83E-07
vg0506420059 sf0506419999 5 6420059 NA 1.84E-07
vg1125256797 sf1124790637 11 25256797 NA 4.97E-07
vg1128439104 sf1127915883 11 28439104 NA 5.56E-07
vg1009825111 sf1009753932 10 9825111 NA 8.72E-07