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Detailed information for vg0123033739:

Variant ID: vg0123033739 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23033739
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: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CTCATGAAGTGATTGGACGACCACGAGAAACGGCCACAAGGCACCGTCAAGGCCTTGGACTCTCACGTCACATGTGAAGTCTGCGACAACACGGGTCATT[C/T]
TGGGAATGACTGCCCGGAAACCCGTGAGGAGGCGATGTACATGGGAAACAACAACAACAACGGGCATCGTCCACAAGGAGGTCAGGGGTGGAACCAACCA

Reverse complement sequence

TGGTTGGTTCCACCCCTGACCTCCTTGTGGACGATGCCCGTTGTTGTTGTTGTTTCCCATGTACATCGCCTCCTCACGGGTTTCCGGGCAGTCATTCCCA[G/A]
AATGACCCGTGTTGTCGCAGACTTCACATGTGACGTGAGAGTCCAAGGCCTTGACGGTGCCTTGTGGCCGTTTCTCGTGGTCGTCCAATCACTTCATGAG

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	90.10%	7.60%	0.55%	1.80%	NA
All Indica	2759	86.40%	12.50%	0.72%	0.36%	NA
All Japonica	1512	94.70%	0.10%	0.33%	4.89%	NA
Aus	269	96.70%	3.30%	0.00%	0.00%	NA
Indica I	595	80.30%	18.00%	1.18%	0.50%	NA
Indica II	465	98.70%	1.10%	0.22%	0.00%	NA
Indica III	913	84.10%	14.90%	0.44%	0.55%	NA
Indica Intermediate	786	86.50%	12.20%	1.02%	0.25%	NA
Temperate Japonica	767	91.40%	0.00%	0.52%	8.08%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	94.60%	0.00%	0.41%	4.98%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	3.30%	1.11%	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
vg0123033739	C -> T	LOC_Os01g40780.1	upstream_gene_variant ; 2126.0bp to feature; MODIFIER	silent_mutation	Average:62.961; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0123033739	C -> T	LOC_Os01g40760.1	downstream_gene_variant ; 2739.0bp to feature; MODIFIER	silent_mutation	Average:62.961; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0123033739	C -> T	LOC_Os01g40770.1	intron_variant ; MODIFIER	silent_mutation	Average:62.961; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0123033739	C -> DEL	N	N	silent_mutation	Average:62.961; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123033739	6.60E-07	NA	mr1598_2	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