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 mr1132 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
vg1215955784 sf1215953080 12 15955784 7.75E-70 4.73E-37
vg1212877317 sf1212874656 12 12877317 5.06E-23 2.60E-09
vg1011512136 sf1011440955 10 11512136 2.74E-20 3.62E-06
vg0500829493 sf0500829475 5 829493 6.57E-20 NA
vg0725525444 sf0725524450 7 25525444 1.10E-19 NA
vg1110282765 sf1110277342 11 10282765 1.24E-19 1.45E-07
vg0920348485 sf0920348004 9 20348485 1.90E-18 3.64E-08
vg1123486862 sf1123020732 11 23486862 1.24E-17 7.19E-07
vg1203326244 sf1203325247 12 3326244 1.50E-17 4.51E-07
vg1117717695 sf1117251551 11 17717695 7.38E-17 8.90E-07
vg1218663003 sf1218634438 12 18663003 1.98E-16 1.16E-13
vg1018571610 sf1018500167 10 18571610 2.83E-16 2.55E-07
vg1006587700 sf1006603323 10 6587700 1.86E-15 9.98E-13
vg0205962645 sf0205962645 2 5962645 1.38E-14 4.16E-07
vg1215852700 sf1215849996 12 15852700 NA 9.30E-16
vg1022588644 sf1022517118 10 22588644 NA 3.70E-14
vg0408293903 sf0408289177 4 8293903 NA 1.87E-09
vg1213186520 sf1213183858 12 13186520 NA 1.13E-08
vg0715496678 sf0715495685 7 15496678 NA 6.65E-08
vg1011512046 sf1011440865 10 11512046 NA 9.04E-08
vg0901555680 sf0901554680 9 1555680 NA 9.23E-08
vg1208048440 sf1208045846 12 8048440 NA 9.59E-08
vg1216136207 sf1216133503 12 16136207 NA 2.96E-07
vg1117387081 sf1116920934 11 17387081 NA 3.39E-07
vg0623791757 sf0623790760 6 23791757 NA 3.69E-07
vg0816293722 sf0816291008 8 16293722 NA 4.13E-07