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Detailed information for vg1001351812:

Variant ID: vg1001351812 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1351812
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTGTCCAGAATTTCAGACTGTCCACACTAAAACAACCATAACTAGAATTCTACTCACCCAATCAGGGTGTACTTTACCAATATGGAAAGCTAAGAAAAA[C/T]
CTCTACAACTTTGTCTATAGGCGGCCTAGCTGTTTCCACTGTTTAACCCGGCCAAAAACAGTTCAATCTATTACTATCCAGATTATGACATAAAAACAAC

Reverse complement sequence

GTTGTTTTTATGTCATAATCTGGATAGTAATAGATTGAACTGTTTTTGGCCGGGTTAAACAGTGGAAACAGCTAGGCCGCCTATAGACAAAGTTGTAGAG[G/A]
TTTTTCTTAGCTTTCCATATTGGTAAAGTACACCCTGATTGGGTGAGTAGAATTCTAGTTATGGTTGTTTTAGTGTGGACAGTCTGAAATTCTGGACAGA

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	58.90%	0.30%	20.31%	20.50%	NA
All Indica	2759	62.40%	0.20%	31.46%	5.94%	NA
All Japonica	1512	48.40%	0.10%	1.59%	49.93%	NA
Aus	269	92.60%	0.40%	6.32%	0.74%	NA
Indica I	595	63.90%	0.20%	26.05%	9.92%	NA
Indica II	465	46.00%	0.40%	46.88%	6.67%	NA
Indica III	913	66.90%	0.00%	30.78%	2.30%	NA
Indica Intermediate	786	65.80%	0.30%	27.23%	6.74%	NA
Temperate Japonica	767	73.80%	0.00%	0.65%	25.55%	NA
Tropical Japonica	504	23.20%	0.00%	2.38%	74.40%	NA
Japonica Intermediate	241	20.30%	0.40%	2.90%	76.35%	NA
VI/Aromatic	96	28.10%	7.30%	33.33%	31.25%	NA
Intermediate	90	58.90%	0.00%	21.11%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001351812	C -> T	LOC_Os10g03190.1	upstream_gene_variant ; 2762.0bp to feature; MODIFIER	silent_mutation	Average:26.705; most accessible tissue: Callus, score: 50.921	N	N	N	N
vg1001351812	C -> T	LOC_Os10g03210.1	upstream_gene_variant ; 3626.0bp to feature; MODIFIER	silent_mutation	Average:26.705; most accessible tissue: Callus, score: 50.921	N	N	N	N
vg1001351812	C -> T	LOC_Os10g03200.1	downstream_gene_variant ; 828.0bp to feature; MODIFIER	silent_mutation	Average:26.705; most accessible tissue: Callus, score: 50.921	N	N	N	N
vg1001351812	C -> T	LOC_Os10g03190-LOC_Os10g03200	intergenic_region ; MODIFIER	silent_mutation	Average:26.705; most accessible tissue: Callus, score: 50.921	N	N	N	N
vg1001351812	C -> DEL	N	N	silent_mutation	Average:26.705; most accessible tissue: Callus, score: 50.921	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001351812	2.62E-06	6.61E-06	mr1171	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