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Detailed information for vg1011367434:

Variant ID: vg1011367434 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11367434
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTGGTTCAGATACTGCGGCGCCCCTTCACCCGCCGAAGTGATGCTGTGGACCATACGGATCTGCATCTTCTTCTGCCGTTTGGACAACTGGCTTGGCGG[G/A]
TCAGCCTTGTAATCACTTGGATTACCCTTCGCTGTACATCTTGGCGTTGTTCGGCTGGGGGTGTTTGCTCCTGAACTGCTTCTCGGGGTGCTTCGACAGT

Reverse complement sequence

ACTGTCGAAGCACCCCGAGAAGCAGTTCAGGAGCAAACACCCCCAGCCGAACAACGCCAAGATGTACAGCGAAGGGTAATCCAAGTGATTACAAGGCTGA[C/T]
CCGCCAAGCCAGTTGTCCAAACGGCAGAAGAAGATGCAGATCCGTATGGTCCACAGCATCACTTCGGCGGGTGAAGGGGCGCCGCAGTATCTGAACCAGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	12.80%	0.30%	27.36%	59.54%	NA
All Indica	2759	1.40%	0.30%	39.51%	58.75%	NA
All Japonica	1512	35.70%	0.30%	0.86%	63.10%	NA
Aus	269	0.70%	0.40%	58.74%	40.15%	NA
Indica I	595	1.30%	0.00%	24.20%	74.45%	NA
Indica II	465	2.20%	0.60%	47.10%	50.11%	NA
Indica III	913	0.90%	0.40%	44.91%	53.78%	NA
Indica Intermediate	786	1.70%	0.30%	40.33%	57.76%	NA
Temperate Japonica	767	68.20%	0.10%	0.26%	31.42%	NA
Tropical Japonica	504	0.60%	0.80%	1.39%	97.22%	NA
Japonica Intermediate	241	5.80%	0.00%	1.66%	92.53%	NA
VI/Aromatic	96	7.30%	0.00%	19.79%	72.92%	NA
Intermediate	90	16.70%	1.10%	14.44%	67.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1011367434	G -> A	LOC_Os10g22010.1	synonymous_variant ; p.Asp814Asp; LOW	synonymous_codon	Average:14.533; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1011367434	G -> DEL	LOC_Os10g22010.1	N	frameshift_variant	Average:14.533; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011367434	1.99E-06	NA	mr1241	Jap_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