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 mr1141 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
vg0602403184 sf0602402185 6 2403184 1.96E-43 3.29E-16
vg0602358935 sf0602357936 6 2358935 2.74E-41 2.09E-16
vg0602401598 sf0602400599 6 2401598 3.93E-41 6.17E-15
vg0602592336 sf0602591337 6 2592336 1.44E-39 2.70E-13
vg0602719571 sf0602718572 6 2719571 1.76E-36 1.52E-06
vg0602642659 sf0602641660 6 2642659 1.57E-33 7.43E-07
vg0729105428 sf0729104436 7 29105428 1.29E-25 5.77E-33
vg0604336913 sf0604335914 6 4336913 8.33E-14 NA
vg0601044442 sf0601043443 6 1044442 1.40E-13 8.90E-07
vg0602936123 sf0602935124 6 2936123 1.44E-13 NA
vg1206967731 sf1206966621 12 6967731 1.50E-13 2.54E-07
vg1201520069 sf1201519069 12 1520069 7.29E-12 1.56E-07
vg1219585537 sf1219557007 12 19585537 2.98E-11 1.23E-10
vg0600576807 sf0600575808 6 576807 8.80E-11 NA
vg1221198057 sf1221164603 12 21198057 2.24E-10 2.29E-14
vg1222473124 sf1222439563 12 22473124 3.34E-10 1.11E-06
vg0219834070 sf0219828202 2 19834070 1.98E-09 1.67E-06
vg0601214662 sf0601213663 6 1214662 2.77E-09 5.66E-07
vg0417556620 sf0417384662 4 17556620 NA 3.25E-09
vg1016323870 sf1016252646 10 16323870 NA 5.70E-09
vg1212357171 sf1212354510 12 12357171 NA 7.03E-08
vg0325722534 sf0325720552 3 25722534 NA 1.93E-07
vg0616470948 sf0616469950 6 16470948 NA 2.90E-07
vg1022381249 sf1022309723 10 22381249 NA 2.97E-07
vg0726950185 sf0726949191 7 26950185 NA 3.57E-07
vg0113416401 sf0113415375 1 13416401 NA 4.44E-07
vg1105430197 sf1105425948 11 5430197 NA 6.01E-07
vg0806359109 sf0806358114 8 6359109 NA 7.20E-07
vg1221718597 sf1221685144 12 21718597 NA 1.70E-06
vg1101299110 sf1101298111 11 1299110 NA 2.05E-06
vg1121399841 sf1120933718 11 21399841 NA 3.22E-06
vg0521119103 sf0521056544 5 21119103 NA 8.39E-06