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Detailed information for vg1000477640:

Variant ID: vg1000477640 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 477640
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

CCTCTCTCAAACCGCGTTTTAGTAACCCTGTATTGCTCTGGTAGTTCAAGCTGCACAACACGGCTAGGTGGAGTTAGCACCCTTCTGGTGTCTATCCATT[C/T]
TCTGTATTGACATCTCCTTGGTGGTTCCTGGGAGAAAAGAATAGATGTGAAGCGAGCAAAGTTAGTAAATGTTGTGAGAAAATAAGGATTCATGATAATC

Reverse complement sequence

GATTATCATGAATCCTTATTTTCTCACAACATTTACTAACTTTGCTCGCTTCACATCTATTCTTTTCTCCCAGGAACCACCAAGGAGATGTCAATACAGA[G/A]
AATGGATAGACACCAGAAGGGTGCTAACTCCACCTAGCCGTGTTGTGCAGCTTGAACTACCAGAGCAATACAGGGTTACTAAAACGCGGTTTGAGAGAGG

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	77.10%	15.20%	0.49%	7.15%	NA
All Indica	2759	70.30%	25.70%	0.47%	3.52%	NA
All Japonica	1512	99.30%	0.10%	0.07%	0.53%	NA
Aus	269	27.90%	0.70%	2.23%	69.14%	NA
Indica I	595	57.30%	42.70%	0.00%	0.00%	NA
Indica II	465	94.60%	4.50%	0.00%	0.86%	NA
Indica III	913	68.10%	25.60%	0.99%	5.26%	NA
Indica Intermediate	786	68.20%	25.60%	0.51%	5.73%	NA
Temperate Japonica	767	99.70%	0.10%	0.00%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	96.30%	0.40%	0.41%	2.90%	NA
VI/Aromatic	96	57.30%	1.00%	1.04%	40.62%	NA
Intermediate	90	84.40%	4.40%	2.22%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000477640	C -> T	LOC_Os10g01740.1	missense_variant ; p.Glu11Lys; MODERATE	nonsynonymous_codon ; E11K	Average:19.597; most accessible tissue: Minghui63 panicle, score: 29.741	benign	1.285	DELETERIOUS	0.00
vg1000477640	C -> DEL	LOC_Os10g01740.1	N	frameshift_variant	Average:19.597; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000477640	NA	1.91E-06	mr1655_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251