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Detailed information for vg0106597852:

Variant ID: vg0106597852 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 6597852
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, C: 0.04, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

GAACAAACGCGCGCTACTCTTTTGACTACTCTCATACACAAACACAACACACACGCACACTATTTGCACGGTCCCTGTACTATGCATGGAGAGTTTGATT[C/G]
GTAGCAACTCCATCCGTTACATATTATAAGTCATTTGATATTTTCCTTAGTTAAAGTTCTTTAGGTTTGCAAAAGGGTCTGTAGCCTAGTGGTTACAAGA

Reverse complement sequence

TCTTGTAACCACTAGGCTACAGACCCTTTTGCAAACCTAAAGAACTTTAACTAAGGAAAATATCAAATGACTTATAATATGTAACGGATGGAGTTGCTAC[G/C]
AATCAAACTCTCCATGCATAGTACAGGGACCGTGCAAATAGTGTGCGTGTGTGTTGTGTTTGTGTATGAGAGTAGTCAAAAGAGTAGCGCGCGTTTGTTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.50%	36.40%	0.06%	0.00%	NA
All Indica	2759	57.70%	42.20%	0.11%	0.00%	NA
All Japonica	1512	87.10%	12.90%	0.00%	0.00%	NA
Aus	269	0.00%	100.00%	0.00%	0.00%	NA
Indica I	595	41.80%	57.80%	0.34%	0.00%	NA
Indica II	465	68.80%	31.20%	0.00%	0.00%	NA
Indica III	913	68.30%	31.70%	0.00%	0.00%	NA
Indica Intermediate	786	50.90%	49.00%	0.13%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	77.00%	23.00%	0.00%	0.00%	NA
Japonica Intermediate	241	69.70%	30.30%	0.00%	0.00%	NA
VI/Aromatic	96	28.10%	71.90%	0.00%	0.00%	NA
Intermediate	90	72.20%	27.80%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0106597852	C -> G	LOC_Os01g12110-LOC_Os01g12120	intergenic_region ; MODIFIER	silent_mutation	Average:55.058; most accessible tissue: Minghui63 root, score: 82.185	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0106597852	NA	2.37E-06	mr1574	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
vg0106597852	2.03E-07	2.03E-07	mr1050_2	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
vg0106597852	NA	4.57E-06	mr1825_2	Ind_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