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 mr1543 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
vg0221812870 sf0221807001 2 21812870 1.06E-17 4.81E-14
vg1117798854 sf1117332710 11 17798854 4.87E-15 NA
vg0221875605 sf0221869736 2 21875605 6.27E-15 4.56E-10
vg1117869490 sf1117403346 11 17869490 8.47E-15 NA
vg1118063449 sf1117597307 11 18063449 1.53E-14 1.37E-06
vg0232210538 sf0232204669 2 32210538 1.88E-14 NA
vg1115275633 sf1114811947 11 15275633 2.32E-14 1.63E-06
vg0221919301 sf0221913432 2 21919301 7.37E-14 3.84E-11
vg1227454410 sf1227420810 12 27454410 1.03E-13 1.59E-07
vg0212332283 sf0212332279 2 12332283 3.54E-13 1.13E-07
vg0920196604 sf0920196123 9 20196604 1.18E-12 3.35E-06
vg1119579328 sf1119113016 11 19579328 1.17E-11 4.37E-07
vg0430514346 sf0430329224 4 30514346 3.70E-11 1.27E-06
vg0141996640 sf0141995597 1 41996640 1.36E-10 3.59E-06
vg0429966299 sf0429781166 4 29966299 3.75E-10 NA
vg1217531096 sf1217525051 12 17531096 5.00E-10 3.51E-06
vg0124882911 sf0124881867 1 24882911 3.26E-09 1.31E-07
vg0221866544 sf0221860675 2 21866544 NA 3.01E-09
vg0234351254 sf0234345385 2 34351254 NA 3.38E-07
vg0402377935 sf0402373530 4 2377935 NA 1.58E-06
vg1001247771 sf1001246748 10 1247771 NA 1.93E-06
vg0707567583 sf0707566588 7 7567583 NA 2.30E-06
vg0221817321 sf0221811452 2 21817321 NA 2.55E-06
vg0110096745 sf0110095721 1 10096745 NA 3.36E-06
vg0129270300 sf0129269255 1 29270300 NA 4.04E-06
vg1105403833 sf1105399584 11 5403833 NA 4.40E-06