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 mr1404 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
vg0719064221 sf0719063228 7 19064221 1.64E-82 2.62E-28
vg0719006702 sf0719005709 7 19006702 1.48E-79 4.54E-29
vg0719088274 sf0719087281 7 19088274 3.04E-73 1.62E-32
vg0917918788 sf0917917787 9 17918788 7.68E-58 NA
vg0305665264 sf0305664264 3 5665264 1.81E-57 NA
vg0705560234 sf0705559235 7 5560234 3.36E-57 NA
vg0626902287 sf0626901290 6 26902287 1.12E-56 NA
vg0719081486 sf0719080493 7 19081486 2.88E-53 8.38E-18
vg0719091461 sf0719090468 7 19091461 NA 8.31E-22
vg0719071513 sf0719070520 7 19071513 NA 8.83E-17
vg0718955684 sf0718954691 7 18955684 NA 6.15E-13
vg0719362195 sf0719361202 7 19362195 NA 2.26E-12
vg0719140918 sf0719139925 7 19140918 NA 5.95E-12
vg0719050776 sf0719049783 7 19050776 NA 7.00E-10
vg0719091007 sf0719090014 7 19091007 NA 4.58E-08
vg0722032999 sf0722032006 7 22032999 NA 9.55E-08
vg1010396385 sf1010325206 10 10396385 NA 1.44E-07
vg1222822194 sf1222788633 12 22822194 NA 1.80E-07
vg1010307395 sf1010236216 10 10307395 NA 1.91E-07
vg0719618102 sf0719617109 7 19618102 NA 5.21E-07
vg0121481145 sf0121480100 1 21481145 NA 6.26E-07
vg0718951050 sf0718950057 7 18951050 NA 8.04E-07
vg1203838792 sf1203837791 12 3838792 NA 8.33E-07
vg1014048599 sf1013977365 10 14048599 NA 9.10E-07
vg0718976518 sf0718975525 7 18976518 NA 1.11E-06
vg0719016083 sf0719015090 7 19016083 NA 1.62E-06
vg1006449338 sf1006464961 10 6449338 NA 1.86E-06
vg0811120813 sf0811119818 8 11120813 NA 1.95E-06
vg0336255999 sf0336248869 3 36255999 NA 2.48E-06
vg0718879158 sf0718878165 7 18879158 NA 4.96E-06