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Detailed information for vg1110994837:

Variant ID: vg1110994837 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10994837
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCACAGCATTGCCTATAGATTTTTAATAGTTAAATCTGAGGTACCTGACATGCATGTTGGTACAATTATGGAGTCTCGTGATGCAACCTTCTTTGAGAG[C/T]
TTTTTCCCAATGAAGGATACACATAGTAGTTCTAGCCAACCCTCTAAAATAATTCCCAGTTCAATCACACCACCAGAACAAACTGAACATACACATGAAC

Reverse complement sequence

GTTCATGTGTATGTTCAGTTTGTTCTGGTGGTGTGATTGAACTGGGAATTATTTTAGAGGGTTGGCTAGAACTACTATGTGTATCCTTCATTGGGAAAAA[G/A]
CTCTCAAAGAAGGTTGCATCACGAGACTCCATAATTGTACCAACATGCATGTCAGGTACCTCAGATTTAACTATTAAAAATCTATAGGCAATGCTGTGGT

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	45.90%	41.70%	12.27%	0.19%	NA
All Indica	2759	18.20%	63.70%	17.80%	0.29%	NA
All Japonica	1512	98.60%	0.90%	0.46%	0.00%	NA
Aus	269	16.00%	58.00%	26.02%	0.00%	NA
Indica I	595	17.80%	61.70%	20.34%	0.17%	NA
Indica II	465	12.00%	69.70%	18.28%	0.00%	NA
Indica III	913	13.50%	70.80%	15.55%	0.22%	NA
Indica Intermediate	786	27.60%	53.60%	18.19%	0.64%	NA
Temperate Japonica	767	98.80%	0.90%	0.26%	0.00%	NA
Tropical Japonica	504	98.20%	1.20%	0.60%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.83%	0.00%	NA
VI/Aromatic	96	89.60%	7.30%	3.12%	0.00%	NA
Intermediate	90	51.10%	37.80%	10.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110994837	C -> T	LOC_Os11g19230.1	synonymous_variant ; p.Ser707Ser; LOW	synonymous_codon	Average:20.405; most accessible tissue: Minghui63 root, score: 31.271	N	N	N	N
vg1110994837	C -> DEL	LOC_Os11g19230.1	N	frameshift_variant	Average:20.405; most accessible tissue: Minghui63 root, score: 31.271	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110994837	4.25E-07	5.08E-06	mr1671	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