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Detailed information for vg0705427326:

Variant ID: vg0705427326 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 5427326
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAGTTTTGACGTGTCACATCGGGTATTATATAGGGTGTCATATGATGTGTTCAGGCACTAATAAAAAAACTAATTACAGAATCCGTCGGTAAACTGTGA[C/G]
ACGAATTTATTAAGCCTAATTAATCCGTTATTAGCTAATGTTTATTGTAGCATCACATTGTCAAATCATGAAGCAATTAGGCTTAAAAGATTCGTCTCGC

Reverse complement sequence

GCGAGACGAATCTTTTAAGCCTAATTGCTTCATGATTTGACAATGTGATGCTACAATAAACATTAGCTAATAACGGATTAATTAGGCTTAATAAATTCGT[G/C]
TCACAGTTTACCGACGGATTCTGTAATTAGTTTTTTTATTAGTGCCTGAACACATCATATGACACCCTATATAATACCCGATGTGACACGTCAAAACTTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.40%	35.20%	0.00%	1.33%	NA
All Indica	2759	97.20%	2.50%	0.00%	0.29%	NA
All Japonica	1512	0.30%	96.30%	0.00%	3.37%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	96.30%	3.40%	0.00%	0.33%	NA
Indica Intermediate	786	96.60%	2.80%	0.00%	0.64%	NA
Temperate Japonica	767	0.10%	94.40%	0.00%	5.48%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	95.40%	0.00%	3.73%	NA
VI/Aromatic	96	3.10%	93.80%	0.00%	3.12%	NA
Intermediate	90	45.60%	53.30%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0705427326	C -> DEL	N	N	silent_mutation	Average:47.535; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0705427326	C -> G	LOC_Os07g10110.1	upstream_gene_variant ; 754.0bp to feature; MODIFIER	silent_mutation	Average:47.535; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0705427326	C -> G	LOC_Os07g10120.1	upstream_gene_variant ; 4227.0bp to feature; MODIFIER	silent_mutation	Average:47.535; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0705427326	C -> G	LOC_Os07g10110-LOC_Os07g10120	intergenic_region ; MODIFIER	silent_mutation	Average:47.535; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0705427326	NA	2.38E-34	mr1081	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
vg0705427326	NA	6.94E-39	mr1082	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
vg0705427326	NA	2.04E-45	mr1092	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
vg0705427326	NA	5.83E-46	mr1152	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
vg0705427326	1.68E-06	NA	mr1549	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
vg0705427326	5.64E-06	NA	mr1550	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
vg0705427326	7.94E-12	NA	mr1757	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
vg0705427326	6.30E-06	NA	mr1757	Jap_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
vg0705427326	NA	8.90E-55	mr1861	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
vg0705427326	NA	8.77E-29	mr1922	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
vg0705427326	NA	3.38E-13	mr1924	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
vg0705427326	NA	4.75E-27	mr1074_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
vg0705427326	NA	4.02E-32	mr1081_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
vg0705427326	NA	1.68E-35	mr1107_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
vg0705427326	NA	3.71E-18	mr1239_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
vg0705427326	NA	2.29E-13	mr1326_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
vg0705427326	NA	4.03E-15	mr1333_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
vg0705427326	NA	8.74E-08	mr1335_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
vg0705427326	NA	3.30E-24	mr1386_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
vg0705427326	2.01E-17	NA	mr1549_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
vg0705427326	2.84E-11	1.37E-11	mr1549_2	Jap_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
vg0705427326	9.97E-13	NA	mr1550_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
vg0705427326	6.32E-08	6.12E-08	mr1550_2	Jap_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
vg0705427326	NA	7.54E-07	mr1623_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
vg0705427326	NA	4.93E-16	mr1686_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
vg0705427326	1.94E-16	NA	mr1757_2	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
vg0705427326	1.26E-09	9.36E-10	mr1757_2	Jap_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