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Detailed information for vg1000821431:

Variant ID: vg1000821431 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 821431
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAAGCTTCTTACTGTAGACAAAGAATTCACCATGGTTGTGGCAGGAAGCATGGGGTACATAGACCCAGTGTTCTATATGACTGGTCACTTAACACAAAA[A/G]
AGTGATGTGTTTAGTTTTGGAGTTGTATTGCTGGAGCTCATCAGCAGAAGGCAAACAATATATGGCAAGAACCGCAGCCTCATTATTGAGTTCCAAGAGG

Reverse complement sequence

CCTCTTGGAACTCAATAATGAGGCTGCGGTTCTTGCCATATATTGTTTGCCTTCTGCTGATGAGCTCCAGCAATACAACTCCAAAACTAAACACATCACT[T/C]
TTTTGTGTTAAGTGACCAGTCATATAGAACACTGGGTCTATGTACCCCATGCTTCCTGCCACAACCATGGTGAATTCTTTGTCTACAGTAAGAAGCTTGG

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	54.10%	12.90%	0.34%	32.65%	NA
All Indica	2759	51.10%	0.70%	0.40%	47.81%	NA
All Japonica	1512	59.50%	38.00%	0.07%	2.45%	NA
Aus	269	65.40%	0.00%	0.37%	34.20%	NA
Indica I	595	37.60%	1.00%	1.01%	60.34%	NA
Indica II	465	78.30%	0.40%	0.00%	21.29%	NA
Indica III	913	50.30%	0.30%	0.11%	49.29%	NA
Indica Intermediate	786	46.20%	1.00%	0.51%	52.29%	NA
Temperate Japonica	767	35.90%	63.60%	0.13%	0.39%	NA
Tropical Japonica	504	95.00%	2.80%	0.00%	2.18%	NA
Japonica Intermediate	241	60.20%	30.30%	0.00%	9.54%	NA
VI/Aromatic	96	12.50%	0.00%	2.08%	85.42%	NA
Intermediate	90	68.90%	15.60%	1.11%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000821431	A -> G	LOC_Os10g02284.1	synonymous_variant ; p.Lys363Lys; LOW	synonymous_codon	Average:29.437; most accessible tissue: Callus, score: 70.507	N	N	N	N
vg1000821431	A -> DEL	LOC_Os10g02284.1	N	frameshift_variant	Average:29.437; most accessible tissue: Callus, score: 70.507	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000821431	3.63E-06	1.62E-06	mr1412	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