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Detailed information for vg0723595937:

Variant ID: vg0723595937 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 23595937
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGCCTGAGATCTGCACCGGGTAGGCGGGTGATCAGGTTTTTGGGGAGTGCCTCCCGCACGACTGCTCATCGCCATGTCTGGAGTTGCTGCCGCCACTG[C/T]
TGGCGGAGGTGGTACGCCACCGCCGACAGGAGCTGGATCTGGATCCGGAGCTGGTGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAGCGGAGGCAAT

Reverse complement sequence

ATTGCCTCCGCTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCACCAGCTCCGGATCCAGATCCAGCTCCTGTCGGCGGTGGCGTACCACCTCCGCCA[G/A]
CAGTGGCGGCAGCAACTCCAGACATGGCGATGAGCAGTCGTGCGGGAGGCACTCCCCAAAAACCTGATCACCCGCCTACCCGGTGCAGATCTCAGGCGAA

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	39.60%	19.70%	5.12%	35.61%	NA
All Indica	2759	9.90%	29.90%	7.97%	52.23%	NA
All Japonica	1512	99.30%	0.50%	0.07%	0.20%	NA
Aus	269	8.20%	5.20%	5.20%	81.41%	NA
Indica I	595	6.60%	14.60%	5.71%	73.11%	NA
Indica II	465	13.50%	13.80%	5.59%	67.10%	NA
Indica III	913	3.80%	54.10%	10.41%	31.65%	NA
Indica Intermediate	786	17.20%	23.00%	8.27%	51.53%	NA
Temperate Japonica	767	99.60%	0.10%	0.13%	0.13%	NA
Tropical Japonica	504	99.60%	0.20%	0.00%	0.20%	NA
Japonica Intermediate	241	97.50%	2.10%	0.00%	0.41%	NA
VI/Aromatic	96	28.10%	68.80%	2.08%	1.04%	NA
Intermediate	90	53.30%	20.00%	5.56%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0723595937	C -> DEL	N	N	silent_mutation	Average:21.66; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg0723595937	C -> T	LOC_Os07g39380.1	downstream_gene_variant ; 1129.0bp to feature; MODIFIER	silent_mutation	Average:21.66; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg0723595937	C -> T	LOC_Os07g39390.1	downstream_gene_variant ; 365.0bp to feature; MODIFIER	silent_mutation	Average:21.66; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg0723595937	C -> T	LOC_Os07g39400.1	downstream_gene_variant ; 2456.0bp to feature; MODIFIER	silent_mutation	Average:21.66; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg0723595937	C -> T	LOC_Os07g39380-LOC_Os07g39390	intergenic_region ; MODIFIER	silent_mutation	Average:21.66; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0723595937	3.93E-07	NA	mr1134_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