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 mr1312 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
vg0321576069 sf0321574579 3 21576069 1.79E-10 1.79E-10
vg0805005643 sf0805004646 8 5005643 6.20E-10 6.20E-10
vg0124420479 sf0124419435 1 24420479 1.50E-09 1.50E-09
vg0805900956 sf0805899959 8 5900956 4.56E-09 4.56E-09
vg0107079035 sf0107078035 1 7079035 5.93E-09 5.93E-09
vg0826077942 sf0826075228 8 26077942 1.17E-08 1.17E-08
vg0329703696 sf0329696736 3 29703696 2.10E-08 2.10E-08
vg0610852582 sf0610851583 6 10852582 7.13E-08 7.13E-08
vg0629600574 sf0629599576 6 29600574 7.20E-08 7.20E-08
vg0138706549 sf0138705506 1 38706549 8.74E-08 8.74E-08
vg0414587628 sf0414578342 4 14587628 8.86E-08 8.86E-08
vg0606109335 sf0606108336 6 6109335 1.22E-07 1.22E-07
vg0604014602 sf0604013603 6 4014602 1.32E-07 1.33E-07
vg0900843381 sf0900842381 9 843381 2.01E-07 2.01E-07
vg0500776377 sf0500776359 5 776377 2.08E-07 2.08E-07
vg0205924397 sf0205924397 2 5924397 2.49E-07 2.49E-07
vg0206578247 sf0206578247 2 6578247 3.19E-07 3.19E-07
vg1013182968 sf1013111738 10 13182968 4.05E-07 4.05E-07
vg0724377253 sf0724376259 7 24377253 4.15E-07 4.15E-07
vg0322174837 sf0322173344 3 22174837 4.84E-07 4.84E-07
vg0706786499 sf0706785504 7 6786499 5.67E-07 5.67E-07