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Detailed information for vg1205884419:

Variant ID: vg1205884419 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5884419
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTCATCATCAAACTGTACCTCCATCGACACTAGGTCGGCAACGATCTCCTTGAAGACCGATATGTGGTTCAACACAGAACCACTCTCCTGCAACTTGTG[T/C]
GAGAATAACTTCATCTTGATATGCATCTTACTGGTTAGATCTTTAGACATGCAGATCGATTCCAGTTTGAGCCAAAGTTCTTCAGCAGTCTTTTCCTGCA

Reverse complement sequence

TGCAGGAAAAGACTGCTGAAGAACTTTGGCTCAAACTGGAATCGATCTGCATGTCTAAAGATCTAACCAGTAAGATGCATATCAAGATGAAGTTATTCTC[A/G]
CACAAGTTGCAGGAGAGTGGTTCTGTGTTGAACCACATATCGGTCTTCAAGGAGATCGTTGCCGACCTAGTGTCGATGGAGGTACAGTTTGATGATGAAG

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	41.10%	12.50%	11.45%	34.96%	NA
All Indica	2759	59.50%	4.00%	16.64%	19.83%	NA
All Japonica	1512	5.80%	30.20%	1.39%	62.70%	NA
Aus	269	62.50%	4.80%	20.07%	12.64%	NA
Indica I	595	8.40%	11.10%	39.16%	41.34%	NA
Indica II	465	78.10%	2.40%	9.03%	10.54%	NA
Indica III	913	85.10%	0.30%	5.15%	9.42%	NA
Indica Intermediate	786	57.50%	3.90%	17.43%	21.12%	NA
Temperate Japonica	767	8.00%	38.60%	1.43%	52.02%	NA
Tropical Japonica	504	4.20%	13.30%	1.39%	81.15%	NA
Japonica Intermediate	241	2.10%	38.60%	1.24%	58.09%	NA
VI/Aromatic	96	13.50%	0.00%	0.00%	86.46%	NA
Intermediate	90	36.70%	11.10%	7.78%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1205884419	T -> C	LOC_Os12g10890.1	synonymous_variant ; p.Ser110Ser; LOW	synonymous_codon	Average:12.431; most accessible tissue: Minghui63 root, score: 23.574	N	N	N	N
vg1205884419	T -> DEL	LOC_Os12g10890.1	N	frameshift_variant	Average:12.431; most accessible tissue: Minghui63 root, score: 23.574	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205884419	4.23E-06	NA	mr1619	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