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Detailed information for vg0721904261:

Variant ID: vg0721904261 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21904261
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCGGCTCCAAGCAAAAGACCACTGGACGGCGACGGCGACAGCGACGGCGACAGCCACGACGACGGCGGAAGGGCGGCGAACTACACGCGCGGCGATAGC[C/T]
GGAACGGAAGGGCGAATAGCTGGATTACAGCTCCGAGGAACGAGGAACGCTAACGACGTGATTAGGGCAGAGAATACGATACAAGTTCGTAGGGCACCAC

Reverse complement sequence

GTGGTGCCCTACGAACTTGTATCGTATTCTCTGCCCTAATCACGTCGTTAGCGTTCCTCGTTCCTCGGAGCTGTAATCCAGCTATTCGCCCTTCCGTTCC[G/A]
GCTATCGCCGCGCGTGTAGTTCGCCGCCCTTCCGCCGTCGTCGTGGCTGTCGCCGTCGCTGTCGCCGTCGCCGTCCAGTGGTCTTTTGCTTGGAGCCGAA

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	44.20%	0.70%	16.86%	38.19%	NA
All Indica	2759	17.10%	0.00%	24.14%	58.72%	NA
All Japonica	1512	96.30%	2.10%	1.46%	0.13%	NA
Aus	269	2.60%	0.00%	37.17%	60.22%	NA
Indica I	595	4.40%	0.00%	11.76%	83.87%	NA
Indica II	465	27.70%	0.00%	22.15%	50.11%	NA
Indica III	913	15.90%	0.00%	35.71%	48.41%	NA
Indica Intermediate	786	21.90%	0.10%	21.25%	56.74%	NA
Temperate Japonica	767	93.10%	3.90%	2.87%	0.13%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	66.70%	0.00%	10.00%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0721904261	C -> DEL	N	N	silent_mutation	Average:43.544; most accessible tissue: Callus, score: 71.506	N	N	N	N
vg0721904261	C -> T	LOC_Os07g36610.1	intron_variant ; MODIFIER	silent_mutation	Average:43.544; most accessible tissue: Callus, score: 71.506	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721904261	NA	4.26E-07	mr1382	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