Search for Variation information by Variation ID:

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Detailed information for vg0138625526:

Variant ID: vg0138625526 (JBrowse)	Variation Type: INDEL
Chromosome: chr01	Position: 38625526
Reference Allele: C	Alternative Allele: CAACTTCTTCCAAAATAAGAAGGGGCCTGTTTGGGGACAAACAGTCCAGCTTT,CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT,T,CAACTTCTTCCAAAATAAAAAGGGGCCTGTTTGGGGACAAACAGTCCAGCTTT,CAACTTCTTCCAAAATAAGAAGGGGCCTGTTTGGGGACAAATAGTCCAGCTTT,CAACTTCTTCCAAAATAAGAAGGGACCTGTTTGGGGACAAACAGTCCAGCTTT
Primary Allele: C	Secondary Allele: CAACTTCTTCCAAAATAAGA AGGGGCCTGTTTGGGGACAA ACAGTCCAGCTTT

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.24, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

GAGGATCAGTTTAACCTATACTCATATTTTAGCCTCGAATCTTGAATCGTAGAGAAATTAATTAAGATGTACTTGAATCTGTTTGGGTAGTTTTTAGCTG[C/CAACTTCTTCCAAAATAAGAAGGGGCCTGTTTGGGGACAAACAGTCCAGCTTT,CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT,T,CAACTTCTTCCAAAATAAAAAGGGGCCTGTTTGGGGACAAACAGTCCAGCTTT,CAACTTCTTCCAAAATAAGAAGGGGCCTGTTTGGGGACAAATAGTCCAGCTTT,CAACTTCTTCCAAAATAAGAAGGGACCTGTTTGGGGACAAACAGTCCAGCTTT]
TGGATCATATTCTGAAAAGCTGCAGTTGTAAAATCTAGAAAATAAACTAGAAGTTAGAACCTAGTAAGCCTAGTTTTTTTTTTGATTCTTAGAAATTGGC

Reverse complement sequence

GCCAATTTCTAAGAATCAAAAAAAAAACTAGGCTTACTAGGTTCTAACTTCTAGTTTATTTTCTAGATTTTACAACTGCAGCTTTTCAGAATATGATCCA[G/AAAGCTGGACTGTTTGTCCCCAAACAGGCCCCTTCTTATTTTGGAAGAAGTTG,AAAGCTGGACTGTTTGTCCCCAAATAGGCCCCTTCTTATTTTGGAAGAAGTTG,A,AAAGCTGGACTGTTTGTCCCCAAACAGGCCCCTTTTTATTTTGGAAGAAGTTG,AAAGCTGGACTATTTGTCCCCAAACAGGCCCCTTCTTATTTTGGAAGAAGTTG,AAAGCTGGACTGTTTGTCCCCAAACAGGTCCCTTCTTATTTTGGAAGAAGTTG]
CAGCTAAAAACTACCCAAACAGATTCAAGTACATCTTAATTAATTTCTCTACGATTCAAGATTCGAGGCTAAAATATGAGTATAGGTTAAACTGATCCTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of CAACTTCTTCCAAAATAAGA AGGGGCCTGTTTGGGGACAA ACAGTCCAGCTTT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.70%	34.30%	0.38%	1.04%	CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 4.66%; T: 0.91%; CAACTTCTTCCAAAATAAAAAGGGGCCTGTTTGGGGACAAACAGTCCAGCTTT: 0.72%; CAACTTCTTCCAAAATAAGAAGGGACCTGTTTGGGGACAAACAGTCCAGCTTT: 0.19%; CAACTTCTTCCAAAATAAGAAGGGGCCTGTTTGGGGACAAATAGTCCAGCTTT: 0.13%
All Indica	2759	40.20%	55.50%	0.54%	0.51%	CAACTTCTTCCAAAATAAAAAGGGGCCTGTTTGGGGACAAACAGTCCAGCTTT: 1.23%; T: 1.16%; CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 0.54%; CAACTTCTTCCAAAATAAGAAGGGACCTGTTTGGGGACAAACAGTCCAGCTTT: 0.33%; CAACTTCTTCCAAAATAAGAAGGGGCCTGTTTGGGGACAAATAGTCCAGCTTT: 0.04%
All Japonica	1512	99.40%	0.10%	0.07%	0.00%	CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 0.40%; CAACTTCTTCCAAAATAAGAAGGGGCCTGTTTGGGGACAAATAGTCCAGCTTT: 0.07%
Aus	269	7.40%	26.00%	0.00%	11.90%	CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 50.56%; T: 2.97%; CAACTTCTTCCAAAATAAGAAGGGGCCTGTTTGGGGACAAATAGTCCAGCTTT: 1.12%
Indica I	595	33.90%	57.50%	1.85%	0.50%	CAACTTCTTCCAAAATAAAAAGGGGCCTGTTTGGGGACAAACAGTCCAGCTTT: 5.04%; T: 1.18%
Indica II	465	95.90%	3.70%	0.00%	0.00%	T: 0.22%; CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 0.22%
Indica III	913	10.60%	85.80%	0.00%	0.55%	T: 1.64%; CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 0.66%; CAACTTCTTCCAAAATAAGAAGGGACCTGTTTGGGGACAAACAGTCCAGCTTT: 0.66%; CAACTTCTTCCAAAATAAAAAGGGGCCTGTTTGGGGACAAACAGTCCAGCTTT: 0.11%
Indica Intermediate	786	46.30%	49.40%	0.51%	0.76%	T: 1.15%; CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 1.02%; CAACTTCTTCCAAAATAAGAAGGGACCTGTTTGGGGACAAACAGTCCAGCTTT: 0.38%; CAACTTCTTCCAAAATAAAAAGGGGCCTGTTTGGGGACAAACAGTCCAGCTTT: 0.38%; CAACTTCTTCCAAAATAAGAAGGGGCCTGTTTGGGGACAAATAGTCCAGCTTT: 0.13%
Temperate Japonica	767	99.70%	0.10%	0.00%	0.00%	CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 0.13%
Tropical Japonica	504	99.60%	0.00%	0.20%	0.00%	CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 0.20%
Japonica Intermediate	241	97.90%	0.00%	0.00%	0.00%	CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 1.66%; CAACTTCTTCCAAAATAAGAAGGGGCCTGTTTGGGGACAAATAGTCCAGCTTT: 0.41%
VI/Aromatic	96	29.20%	3.10%	1.04%	1.04%	CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 62.50%; T: 2.08%; CAACTTCTTCCAAAATAAGAAGGGGCCTGTTTGGGGACAAATAGTCCAGCTTT: 1.04%
Intermediate	90	73.30%	18.90%	1.11%	2.22%	CAACTTCTTCCAAAATAAGAAGGGGCCTATTTGGGGACAAACAGTCCAGCTTT: 3.33%; T: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0138625526	C -> T	LOC_Os01g66500.1	upstream_gene_variant ; 1690.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> T	LOC_Os01g66510.1	upstream_gene_variant ; 2220.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> T	LOC_Os01g66500-LOC_Os01g66510	intergenic_region ; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> DEL	N	N	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGGCCTGT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66500.1	upstream_gene_variant ; 1691.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGGCCTGT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66510.1	upstream_gene_variant ; 2219.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGGCCTGT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66500-LOC_Os01g66510	intergenic_region ; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAAAAGGGGCCTGT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66500.1	upstream_gene_variant ; 1691.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAAAAGGGGCCTGT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66510.1	upstream_gene_variant ; 2219.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAAAAGGGGCCTGT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66500-LOC_Os01g66510	intergenic_region ; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGGCCTAT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66500.1	upstream_gene_variant ; 1691.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGGCCTAT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66510.1	upstream_gene_variant ; 2219.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGGCCTAT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66500-LOC_Os01g66510	intergenic_region ; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGACCTGT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66500.1	upstream_gene_variant ; 1691.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGACCTGT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66510.1	upstream_gene_variant ; 2219.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGACCTGT TTGGGGACAAACAGTCCAGCTTT	LOC_Os01g66500-LOC_Os01g66510	intergenic_region ; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGGCCTGT TTGGGGACAAATAGTCCAGCTTT	LOC_Os01g66500.1	upstream_gene_variant ; 1691.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGGCCTGT TTGGGGACAAATAGTCCAGCTTT	LOC_Os01g66510.1	upstream_gene_variant ; 2219.0bp to feature; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N
vg0138625526	C -> CAACTTCTTCCAAAATAAGAAGGGGCCTGT TTGGGGACAAATAGTCCAGCTTT	LOC_Os01g66500-LOC_Os01g66510	intergenic_region ; MODIFIER	silent_mutation	Average:90.286; most accessible tissue: Callus, score: 99.377	N	N	N	N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg0138625526	C	CAACT*	-0.27	-0.32	-0.2	-0.45	-0.19	-0.13
vg0138625526	C	T	-0.03	-0.02	-0.02	-0.01	-0.02	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0138625526	NA	5.78E-20	Plant_height	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0138625526	NA	7.01E-20	Plant_height	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0138625526	NA	1.73E-06	mr1003	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.36E-07	mr1013	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.96E-07	mr1021	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.52E-08	mr1031	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	3.16E-06	mr1034	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.44E-06	mr1050	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.44E-07	mr1051	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	7.02E-07	mr1056	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	3.66E-08	mr1059	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.22E-07	mr1066	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.39E-09	mr1143	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.18E-09	mr1163	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.65E-09	mr1167	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	4.22E-08	mr1192	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	6.01E-08	mr1192	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	3.43E-07	mr1324	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	6.57E-06	mr1325	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	4.13E-06	mr1335	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.07E-07	mr1477	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.64E-06	mr1479	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	3.62E-06	mr1479	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	5.37E-07	mr1532	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	4.52E-15	mr1535	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	5.00E-10	mr1535	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	4.91E-06	mr1552	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.50E-08	mr1574	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	8.34E-06	mr1621	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	7.62E-07	mr1621	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.59E-06	mr1677	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.64E-07	mr1690	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	3.02E-06	4.46E-07	mr1755	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.80E-06	mr1755	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	4.52E-07	mr1835	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	6.53E-08	mr1942	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	9.77E-06	mr1942	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.60E-06	mr1950	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	3.51E-06	mr1975	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.27E-16	mr1995	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.02E-10	mr1995	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.55E-06	mr1060_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	8.74E-06	mr1060_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.03E-06	mr1265_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.84E-07	mr1268_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.83E-07	mr1296_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	6.02E-06	mr1296_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.22E-13	mr1327_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.28E-14	mr1327_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.23E-11	mr1352_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	1.29E-07	mr1360_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.48E-07	mr1360_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	5.68E-10	mr1378_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.44E-06	mr1378_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.34E-07	mr1454_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	7.58E-07	mr1550_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	3.04E-11	mr1627_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	7.12E-07	mr1653_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.44E-06	mr1882_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	4.00E-07	mr1895_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	3.03E-06	mr1899_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	7.56E-06	mr1899_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	3.57E-06	mr1971_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	2.48E-08	mr1977_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0138625526	NA	5.77E-06	mr1977_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251