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Detailed information for vg0231359843:

Variant ID: vg0231359843 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 31359843
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCGACCGGACGAGACGCACTGTCTCATCCGTGTCGTTTGAGAAGCACTCACTTAGTCGTTTTTAGAAAAGAGTTCAAATAAAATCAATTGCAAAAACAA[T/C]
AGCCTTTCTTTGAAGCCTGCATTAAACACTTATTTCCCATAGCTTGCTGAGTACTCCCGTACTCACCCTTGCTCTATATAAATAATCCCCCCCAGTTGCT

Reverse complement sequence

AGCAACTGGGGGGGATTATTTATATAGAGCAAGGGTGAGTACGGGAGTACTCAGCAAGCTATGGGAAATAAGTGTTTAATGCAGGCTTCAAAGAAAGGCT[A/G]
TTGTTTTTGCAATTGATTTTATTTGAACTCTTTTCTAAAAACGACTAAGTGAGTGCTTCTCAAACGACACGGATGAGACAGTGCGTCTCGTCCGGTCGGA

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	49.70%	0.00%	24.33%	25.98%	NA
All Indica	2759	23.70%	0.00%	34.94%	41.36%	NA
All Japonica	1512	99.60%	0.00%	0.13%	0.26%	NA
Aus	269	10.80%	0.00%	61.71%	27.51%	NA
Indica I	595	6.60%	0.00%	25.71%	67.73%	NA
Indica II	465	37.60%	0.20%	30.75%	31.40%	NA
Indica III	913	24.00%	0.00%	42.28%	33.73%	NA
Indica Intermediate	786	28.00%	0.00%	35.88%	36.13%	NA
Temperate Japonica	767	99.50%	0.00%	0.13%	0.39%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	73.30%	0.00%	16.67%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0231359843	T -> DEL	N	N	silent_mutation	Average:8.383; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N
vg0231359843	T -> C	LOC_Os02g51230-LOC_Os02g51240	intergenic_region ; MODIFIER	silent_mutation	Average:8.383; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0231359843	4.27E-07	1.19E-07	mr1011	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