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Detailed information for vg1014032310:

Variant ID: vg1014032310 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14032310
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCCGTGTCGAAACACGGATGACCTCACCAAGAAGGCTAATCCCTGTTTGCCAATCGAAGAACACAAACAAGAACGAGATAGAAAAACAACCAAAATTG[C/T]
AGATGAATGATTAAGCTCATGAGTTGGGGTCTTACAAACCGATCTAGCGGCGAAACTGTTCTCGACAAATTAATCTAAGCAAAACCCGACTCTAAACGAT

Reverse complement sequence

ATCGTTTAGAGTCGGGTTTTGCTTAGATTAATTTGTCGAGAACAGTTTCGCCGCTAGATCGGTTTGTAAGACCCCAACTCATGAGCTTAATCATTCATCT[G/A]
CAATTTTGGTTGTTTTTCTATCTCGTTCTTGTTTGTGTTCTTCGATTGGCAAACAGGGATTAGCCTTCTTGGTGAGGTCATCCGTGTTTCGACACGGGTG

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	44.90%	1.10%	45.49%	8.46%	NA
All Indica	2759	15.90%	1.80%	71.58%	10.66%	NA
All Japonica	1512	99.50%	0.10%	0.33%	0.13%	NA
Aus	269	5.60%	0.70%	55.76%	37.92%	NA
Indica I	595	7.60%	3.00%	72.27%	17.14%	NA
Indica II	465	14.40%	0.20%	74.19%	11.18%	NA
Indica III	913	24.10%	1.30%	67.03%	7.56%	NA
Indica Intermediate	786	13.60%	2.50%	74.81%	9.03%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.40%	0.40%	NA
Japonica Intermediate	241	98.80%	0.40%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	0.00%	22.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1014032310	C -> T	LOC_Os10g26780-LOC_Os10g26800	intergenic_region ; MODIFIER	silent_mutation	Average:10.06; most accessible tissue: Callus, score: 26.472	N	N	N	N
vg1014032310	C -> DEL	N	N	silent_mutation	Average:10.06; most accessible tissue: Callus, score: 26.472	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014032310	7.59E-06	6.07E-06	mr1352	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