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 mr1648 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
vg0717125826 sf0717124833 7 17125826 3.64E-11 7.59E-07
vg1111961036 sf1111955353 11 11961036 7.95E-10 1.87E-06
vg0319113443 sf0319112203 3 19113443 2.20E-09 2.02E-07
vg0503163550 sf0503163526 5 3163550 8.01E-09 1.49E-06
vg0335018170 sf0335011040 3 35018170 8.20E-09 3.76E-07
vg0334677333 sf0334670203 3 34677333 9.01E-09 3.00E-07
vg0718144292 sf0718143299 7 18144292 3.64E-08 7.24E-07
vg1207346320 sf1207343727 12 7346320 5.85E-08 1.13E-06
vg1114628121 sf1114164439 11 14628121 6.17E-08 6.33E-08
vg0403204105 sf0403199708 4 3204105 7.12E-08 2.87E-06
vg0203357479 sf0203357477 2 3357479 7.55E-08 1.20E-06
vg0308084937 sf0308083875 3 8084937 1.32E-07 2.90E-06
vg0610420020 sf0610419021 6 10420020 2.27E-07 1.46E-06
vg1227404000 sf1227370400 12 27404000 3.85E-07 3.14E-06
vg1001023555 sf1001022531 10 1023555 4.46E-07 2.54E-06
vg0232481318 sf0232475449 2 32481318 4.93E-07 2.07E-06
vg1121912359 sf1121446230 11 21912359 7.52E-07 2.32E-06
vg0223757416 sf0223751547 2 23757416 8.74E-07 NA
vg0701188868 sf0701187868 7 1188868 1.01E-06 4.27E-06
vg1116087691 sf1115622563 11 16087691 1.43E-06 1.23E-06
vg0221872725 sf0221866856 2 21872725 NA 3.40E-08
vg0127315416 sf0127314372 1 27315416 NA 3.38E-07
vg0717126175 sf0717125182 7 17126175 NA 3.56E-07
vg0219777610 sf0219771742 2 19777610 NA 4.63E-07
vg0127319721 sf0127318677 1 27319721 NA 5.60E-07
vg0401209853 sf0401205403 4 1209853 NA 6.47E-07
vg1009605363 sf1009534184 10 9605363 NA 9.45E-07
vg0827295276 sf0827292562 8 27295276 NA 1.90E-06
vg0431043984 sf0430858869 4 31043984 NA 2.32E-06