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Detailed information for vg0801252977:

Variant ID: vg0801252977 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1252977
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCCACATACCTGCGGTCAGACCGGCCCTACTAGCCGGTCAGACCGCCCACACACCTGTGGTCTGACCGGCCCTGTGAAGGAAACCCGTCACTTTCCAAA[C/T]
TTTGGCAATTTTCCCCTATTTCGTCTATAGGTGTCAAATTTGGGTGTAAACAGATTTCAGATTCACTAGCATCAACTTTTGCCCTAATTTCCTCGCTCCT

Reverse complement sequence

AGGAGCGAGGAAATTAGGGCAAAAGTTGATGCTAGTGAATCTGAAATCTGTTTACACCCAAATTTGACACCTATAGACGAAATAGGGGAAAATTGCCAAA[G/A]
TTTGGAAAGTGACGGGTTTCCTTCACAGGGCCGGTCAGACCACAGGTGTGTGGGCGGTCTGACCGGCTAGTAGGGCCGGTCTGACCGCAGGTATGTGGGC

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	68.70%	2.10%	7.41%	21.77%	NA
All Indica	2759	78.40%	0.30%	7.76%	13.56%	NA
All Japonica	1512	55.80%	5.10%	4.70%	34.46%	NA
Aus	269	35.30%	3.30%	21.93%	39.41%	NA
Indica I	595	70.80%	0.00%	8.57%	20.67%	NA
Indica II	465	82.60%	0.40%	5.59%	11.40%	NA
Indica III	913	81.80%	0.80%	5.91%	11.50%	NA
Indica Intermediate	786	77.60%	0.00%	10.56%	11.83%	NA
Temperate Japonica	767	61.30%	9.80%	1.30%	27.64%	NA
Tropical Japonica	504	34.30%	0.00%	11.31%	54.37%	NA
Japonica Intermediate	241	83.00%	0.80%	1.66%	14.52%	NA
VI/Aromatic	96	95.80%	0.00%	1.04%	3.12%	NA
Intermediate	90	61.10%	5.60%	5.56%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0801252977	C -> T	LOC_Os08g02909.1	upstream_gene_variant ; 1671.0bp to feature; MODIFIER	silent_mutation	Average:30.277; most accessible tissue: Callus, score: 54.894	N	N	N	N
vg0801252977	C -> T	LOC_Os08g02904.1	downstream_gene_variant ; 2619.0bp to feature; MODIFIER	silent_mutation	Average:30.277; most accessible tissue: Callus, score: 54.894	N	N	N	N
vg0801252977	C -> T	LOC_Os08g02904-LOC_Os08g02909	intergenic_region ; MODIFIER	silent_mutation	Average:30.277; most accessible tissue: Callus, score: 54.894	N	N	N	N
vg0801252977	C -> DEL	N	N	silent_mutation	Average:30.277; most accessible tissue: Callus, score: 54.894	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801252977	2.77E-06	NA	mr1471	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