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 mr1871 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 4.91E-17 4.87E-09
vg0221860877 sf0221855008 2 21860877 4.22E-16 6.91E-11
vg0629150340 sf0629149342 6 29150340 1.98E-11 1.02E-07
vg0310049531 sf0310048467 3 10049531 1.69E-10 9.89E-06
vg0309968802 sf0309967738 3 9968802 2.77E-10 1.44E-07
vg1119474674 sf1119008362 11 19474674 5.60E-10 1.10E-06
vg0113615431 sf0113614405 1 13615431 7.05E-10 8.68E-07
vg1219030340 sf1219001775 12 19030340 1.82E-09 4.61E-06
vg1105927401 sf1105923153 11 5927401 2.26E-08 1.19E-06
vg1226733008 sf1226699406 12 26733008 3.21E-08 3.87E-07
vg0223246627 sf0223240758 2 23246627 2.44E-07 4.97E-06
vg0136491474 sf0136490431 1 36491474 3.00E-07 2.29E-07
vg0128504465 sf0128503420 1 28504465 3.27E-07 6.55E-07
vg0300021861 sf0300020861 3 21861 5.15E-07 3.02E-06
vg0332706732 sf0332699603 3 32706732 6.83E-07 6.21E-07
vg1214795994 sf1214793335 12 14795994 8.61E-07 3.59E-06
vg1121372738 sf1120906615 11 21372738 2.31E-06 3.36E-06
vg1127357348 sf1126885735 11 27357348 6.67E-06 7.95E-07
vg0325079496 sf0325077577 3 25079496 8.41E-06 4.54E-07
vg0114284775 sf0114283749 1 14284775 8.49E-06 NA
vg0212787331 sf0212787327 2 12787331 NA 1.98E-06