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Detailed information for vg0702355371:

Variant ID: vg0702355371 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 2355371
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:

GCTGTCTATTTCTAGTCAGAAAAAGTGCACCGGAGGTCCCTGAACTTGTCACCGAGATACGAAAACGTCCTCAAACCGCAAAACCAAATATATGTGGTCC[C/T]
TTAACTATAGAAAACTGGTCACCCAAGGTCCTTCGGTGGTTTTGACCCCGGTTTTGGTCTACGTGGCGGCTAAGTCAGTGTGGGACCCACCTGTCAGCAT

Reverse complement sequence

ATGCTGACAGGTGGGTCCCACACTGACTTAGCCGCCACGTAGACCAAAACCGGGGTCAAAACCACCGAAGGACCTTGGGTGACCAGTTTTCTATAGTTAA[G/A]
GGACCACATATATTTGGTTTTGCGGTTTGAGGACGTTTTCGTATCTCGGTGACAAGTTCAGGGACCTCCGGTGCACTTTTTCTGACTAGAAATAGACAGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.70%	14.60%	12.76%	39.95%	NA
All Indica	2759	18.70%	4.40%	16.71%	60.17%	NA
All Japonica	1512	63.40%	31.10%	4.70%	0.79%	NA
Aus	269	13.40%	1.10%	21.93%	63.57%	NA
Indica I	595	21.00%	12.60%	14.79%	51.60%	NA
Indica II	465	22.40%	2.40%	16.56%	58.71%	NA
Indica III	913	15.30%	1.20%	17.20%	66.27%	NA
Indica Intermediate	786	18.70%	3.20%	17.68%	60.43%	NA
Temperate Japonica	767	92.30%	4.60%	3.13%	0.00%	NA
Tropical Japonica	504	31.50%	62.10%	3.97%	2.38%	NA
Japonica Intermediate	241	38.20%	50.60%	11.20%	0.00%	NA
VI/Aromatic	96	1.00%	71.90%	3.12%	23.96%	NA
Intermediate	90	37.80%	27.80%	10.00%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0702355371	C -> DEL	N	N	silent_mutation	Average:21.509; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N
vg0702355371	C -> T	LOC_Os07g05220.1	downstream_gene_variant ; 2584.0bp to feature; MODIFIER	silent_mutation	Average:21.509; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N
vg0702355371	C -> T	LOC_Os07g05230.1	downstream_gene_variant ; 3611.0bp to feature; MODIFIER	silent_mutation	Average:21.509; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N
vg0702355371	C -> T	LOC_Os07g05210-LOC_Os07g05220	intergenic_region ; MODIFIER	silent_mutation	Average:21.509; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0702355371	NA	2.07E-06	mr1056	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
vg0702355371	NA	5.24E-07	mr1668	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
vg0702355371	NA	4.43E-06	mr1780	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
vg0702355371	NA	3.91E-06	mr1871	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
vg0702355371	NA	4.27E-07	mr1401_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
vg0702355371	NA	5.01E-12	mr1410_2	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
vg0702355371	NA	5.84E-07	mr1554_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
vg0702355371	NA	1.24E-06	mr1860_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
vg0702355371	NA	2.53E-07	mr1866_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