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 1.49E-30 1.49E-20
vg0221860877 sf0221855008 2 21860877 4.38E-23 1.08E-18
vg0132071481 sf0132070437 1 32071481 6.16E-14 NA
vg1114800054 sf1114336368 11 14800054 9.17E-13 NA
vg1117896001 sf1117429859 11 17896001 1.60E-12 NA
vg1023076412 sf1023004885 10 23076412 1.62E-12 NA
vg0222002131 sf0221996262 2 22002131 5.54E-12 5.25E-09
vg0102765446 sf0102764446 1 2765446 1.50E-11 NA
vg0402662040 sf0402657644 4 2662040 2.92E-11 4.55E-07
vg0430557936 sf0430372811 4 30557936 8.25E-11 2.82E-06
vg0127858725 sf0127857681 1 27858725 4.54E-10 1.18E-07
vg0212332283 sf0212332279 2 12332283 9.88E-10 3.92E-08
vg0629150340 sf0629149342 6 29150340 1.54E-09 2.07E-06
vg0205296239 sf0205296238 2 5296239 1.59E-09 1.29E-06
vg0212316464 sf0212316460 2 12316464 2.11E-09 3.93E-07
vg0216185343 sf0216179473 2 16185343 3.85E-09 3.03E-08
vg0134494458 sf0134493415 1 34494458 8.23E-09 2.03E-06
vg1106632830 sf1106628583 11 6632830 1.11E-08 6.93E-08
vg0527173808 sf0527111164 5 27173808 2.63E-08 3.66E-07
vg0904680838 sf0904679838 9 4680838 3.83E-08 6.65E-07
vg0113669976 sf0113668950 1 13669976 4.29E-08 1.24E-06
vg0221815577 sf0221809708 2 21815577 NA 4.00E-08
vg0136800566 sf0136799523 1 36800566 NA 1.35E-07
vg1127358883 sf1126887270 11 27358883 NA 2.93E-07
vg0205347525 sf0205347525 2 5347525 NA 7.49E-07
vg0214541889 sf0214536019 2 14541889 NA 8.79E-07
vg1126133720 sf1125662134 11 26133720 NA 1.03E-06
vg0401517512 sf0401513062 4 1517512 NA 1.80E-06
vg1226733008 sf1226699406 12 26733008 NA 1.99E-06
vg0300021861 sf0300020861 3 21861 NA 2.48E-06