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 mr1178 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
vg1215965939 sf1215963235 12 15965939 7.44E-141 2.10E-42
vg1210219854 sf1210217266 12 10219854 9.37E-86 7.13E-07
vg1210216877 sf1210214289 12 10216877 1.12E-82 2.16E-07
vg0217071443 sf0217065573 2 17071443 5.54E-68 NA
vg0217044495 sf0217038625 2 17044495 2.34E-67 2.77E-07
vg1212938220 sf1212935559 12 12938220 2.40E-66 8.93E-09
vg1224007541 sf1223973994 12 24007541 9.59E-66 NA
vg1223855613 sf1223822066 12 23855613 2.50E-62 2.56E-07
vg1215872322 sf1215869618 12 15872322 NA 1.16E-21
vg1215970855 sf1215968151 12 15970855 NA 1.78E-12
vg0610620315 sf0610619316 6 10620315 NA 8.52E-10
vg1215871822 sf1215869118 12 15871822 NA 5.63E-09
vg1219118839 sf1219090275 12 19118839 NA 5.09E-08
vg1216470148 sf1216467441 12 16470148 NA 8.89E-08
vg1215182739 sf1215180075 12 15182739 NA 8.99E-08
vg1018726980 sf1018655537 10 18726980 NA 1.43E-07
vg1215962650 sf1215959946 12 15962650 NA 2.16E-06
vg0605135820 sf0605134821 6 5135820 NA 2.25E-06
vg1115582589 sf1115118901 11 15582589 NA 2.45E-06
vg1216151894 sf1216149190 12 16151894 NA 2.87E-06
vg0918927566 sf0918926566 9 18927566 NA 3.97E-06
vg0807147308 sf0807146313 8 7147308 NA 4.48E-06