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 mr1113 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
vg0222679274 sf0222673405 2 22679274 4.92E-49 8.18E-24
vg0222687716 sf0222681847 2 22687716 3.68E-48 1.54E-25
vg1110425815 sf1110420360 11 10425815 9.07E-27 1.98E-09
vg0505887711 sf0505887649 5 5887711 1.46E-25 2.77E-08
vg0526722696 sf0526660054 5 26722696 2.58E-25 NA
vg0518201525 sf0518141011 5 18201525 1.65E-24 6.75E-06
vg0818212763 sf0818210050 8 18212763 3.97E-24 3.76E-08
vg0306047262 sf0306046262 3 6047262 1.13E-22 2.64E-07
vg0922708358 sf0922707877 9 22708358 2.72E-21 3.25E-07
vg0907026290 sf0907025290 9 7026290 1.48E-20 1.48E-07
vg1117963441 sf1117497299 11 17963441 1.35E-19 1.40E-07
vg0616706040 sf0616705042 6 16706040 3.41E-18 3.22E-07
vg0709372324 sf0709371330 7 9372324 2.74E-17 2.20E-07
vg0222948971 sf0222943102 2 22948971 NA 1.33E-11
vg0222722554 sf0222716685 2 22722554 NA 5.27E-11
vg0224323955 sf0224318086 2 24323955 NA 4.34E-09
vg0805024489 sf0805023492 8 5024489 NA 1.48E-08
vg1016331604 sf1016260380 10 16331604 NA 1.80E-08
vg0315642911 sf0315641558 3 15642911 NA 4.47E-08
vg0119009306 sf0119008261 1 19009306 NA 4.63E-08
vg0222671765 sf0222665896 2 22671765 NA 6.21E-08
vg0431376032 sf0431190928 4 31376032 NA 9.85E-08
vg1204507349 sf1204506337 12 4507349 NA 1.05E-07
vg1000205246 sf1000204246 10 205246 NA 1.17E-07
vg0914982012 sf0914981011 9 14982012 NA 1.19E-07
vg1005950387 sf1005966925 10 5950387 NA 1.93E-07
vg0226543196 sf0226537327 2 26543196 NA 2.31E-07
vg0709453116 sf0709452122 7 9453116 NA 3.04E-07
vg0220979533 sf0220973665 2 20979533 NA 6.82E-07
vg1204500771 sf1204499759 12 4500771 NA 1.19E-06
vg1006545773 sf1006561396 10 6545773 NA 4.55E-06
vg0118946335 sf0118945290 1 18946335 NA 6.47E-06