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Detailed information for vg0702624412:

Variant ID: vg0702624412 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 2624412
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATCTGCAGTACGTGGCATGCATTACATATATTTAAATATGTTAATTAATTCGATCTGGATTAATCAAAATTAACATATCTCTATCTCTACTACTTAAAA[C/A]
ATAAGAGGTGCTTCCATTGTCCGTCAAAAAAATCGGGCGAAAAAAACCAAATTTATCCGATCTAAAAAACTGAGCGAAAGAAAACGTCCAGAAAAAAGAG

Reverse complement sequence

CTCTTTTTTCTGGACGTTTTCTTTCGCTCAGTTTTTTAGATCGGATAAATTTGGTTTTTTTCGCCCGATTTTTTTGACGGACAATGGAAGCACCTCTTAT[G/T]
TTTTAAGTAGTAGAGATAGAGATATGTTAATTTTGATTAATCCAGATCGAATTAATTAACATATTTAAATATATGTAATGCATGCCACGTACTGCAGATT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.60%	10.30%	3.09%	0.00%	NA
All Indica	2759	98.60%	0.80%	0.54%	0.00%	NA
All Japonica	1512	61.40%	30.30%	8.33%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.80%	2.70%	1.51%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	0.50%	0.76%	0.00%	NA
Temperate Japonica	767	39.60%	47.20%	13.17%	0.00%	NA
Tropical Japonica	504	94.20%	3.20%	2.58%	0.00%	NA
Japonica Intermediate	241	61.80%	33.20%	4.98%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	6.70%	5.56%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0702624412	C -> A	LOC_Os07g05600.1	upstream_gene_variant ; 3941.0bp to feature; MODIFIER	silent_mutation	Average:29.358; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0702624412	C -> A	LOC_Os07g05590.1	intron_variant ; MODIFIER	silent_mutation	Average:29.358; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0702624412	NA	1.44E-06	mr1206	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
vg0702624412	NA	8.92E-07	mr1229	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
vg0702624412	1.71E-06	2.39E-07	mr1596	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
vg0702624412	6.43E-06	7.02E-08	mr1596	Jap_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
vg0702624412	NA	1.24E-07	mr1763	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
vg0702624412	NA	5.92E-06	mr1763	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
vg0702624412	NA	9.81E-06	mr1775	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
vg0702624412	4.46E-06	NA	mr1789	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
vg0702624412	NA	3.23E-07	mr1880	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
vg0702624412	NA	7.63E-08	mr1137_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
vg0702624412	NA	8.08E-06	mr1617_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
vg0702624412	NA	1.46E-08	mr1880_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
vg0702624412	NA	4.23E-07	mr1880_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