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Detailed information for vg0620397747:

Variant ID: vg0620397747 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20397747
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAAAAGGGGTTCGATGTTTGAAAAATCTGCAGCTGATGGGATCAGCTAGGCCCGGGTGGCCGTTTGAAAAGTTGTTGGCCCGGGTGGCCGTTTGAAAAG[T/C]
TGTTTGCCCGGGTGGCCGTTTGAAAAGCTGTTGGCTGGGTGCCAACCTTGTTGCAATCCTAAAGACTGATACATTGCACATACTCCGACCGGACGAGACG

Reverse complement sequence

CGTCTCGTCCGGTCGGAGTATGTGCAATGTATCAGTCTTTAGGATTGCAACAAGGTTGGCACCCAGCCAACAGCTTTTCAAACGGCCACCCGGGCAAACA[A/G]
CTTTTCAAACGGCCACCCGGGCCAACAACTTTTCAAACGGCCACCCGGGCCTAGCTGATCCCATCAGCTGCAGATTTTTCAAACATCGAACCCCTTTTCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.60%	0.30%	51.57%	17.54%	NA
All Indica	2759	6.60%	0.40%	76.59%	16.49%	NA
All Japonica	1512	80.00%	0.00%	2.31%	17.72%	NA
Aus	269	4.80%	1.90%	72.12%	21.19%	NA
Indica I	595	4.20%	0.00%	62.69%	33.11%	NA
Indica II	465	8.00%	0.00%	78.28%	13.76%	NA
Indica III	913	7.60%	0.90%	85.98%	5.59%	NA
Indica Intermediate	786	6.40%	0.30%	75.19%	18.19%	NA
Temperate Japonica	767	85.10%	0.00%	1.04%	13.82%	NA
Tropical Japonica	504	88.90%	0.00%	3.57%	7.54%	NA
Japonica Intermediate	241	44.80%	0.00%	3.73%	51.45%	NA
VI/Aromatic	96	4.20%	1.00%	63.54%	31.25%	NA
Intermediate	90	41.10%	0.00%	37.78%	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
vg0620397747	T -> C	LOC_Os06g35050.1	upstream_gene_variant ; 2600.0bp to feature; MODIFIER	silent_mutation	Average:20.924; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0620397747	T -> C	LOC_Os06g35040.1	downstream_gene_variant ; 3064.0bp to feature; MODIFIER	silent_mutation	Average:20.924; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0620397747	T -> C	LOC_Os06g35040-LOC_Os06g35050	intergenic_region ; MODIFIER	silent_mutation	Average:20.924; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0620397747	T -> DEL	N	N	silent_mutation	Average:20.924; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620397747	1.54E-06	NA	mr1788_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