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Detailed information for vg1006197301:

Variant ID: vg1006197301 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6197301
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTTAATTTCTCATTAGCCGATCATAATCAATCTTATCTTATATTTCTCTTTTTGCAGCCTCCTCCTGCTCCCTCTTCTCCTGTTCAACAACCATCAAG[T/C]
AATCAAACTCCATCGGCTGTAGGGAGTCATCATGTTGAAGAAGAGGTTCAACCAGCTGCCCCTGCTATCCCAGTAAGTTTTCTTTGGCACAAATACTGAG

Reverse complement sequence

CTCAGTATTTGTGCCAAAGAAAACTTACTGGGATAGCAGGGGCAGCTGGTTGAACCTCTTCTTCAACATGATGACTCCCTACAGCCGATGGAGTTTGATT[A/G]
CTTGATGGTTGTTGAACAGGAGAAGAGGGAGCAGGAGGAGGCTGCAAAAAGAGAAATATAAGATAAGATTGATTATGATCGGCTAATGAGAAATTAAGAA

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	83.90%	12.80%	0.04%	3.30%	NA
All Indica	2759	99.40%	0.60%	0.00%	0.00%	NA
All Japonica	1512	51.90%	38.20%	0.07%	9.92%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.80%	0.00%	0.00%	NA
Temperate Japonica	767	24.60%	57.60%	0.13%	17.60%	NA
Tropical Japonica	504	93.80%	6.00%	0.00%	0.20%	NA
Japonica Intermediate	241	50.60%	43.60%	0.00%	5.81%	NA
VI/Aromatic	96	94.80%	0.00%	1.04%	4.17%	NA
Intermediate	90	84.40%	13.30%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1006197301	T -> C	LOC_Os10g11180.1	synonymous_variant ; p.Ser656Ser; LOW	synonymous_codon	Average:41.933; most accessible tissue: Zhenshan97 young leaf, score: 62.534	N	N	N	N
vg1006197301	T -> DEL	LOC_Os10g11180.1	N	frameshift_variant	Average:41.933; most accessible tissue: Zhenshan97 young leaf, score: 62.534	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1006197301	5.06E-07	NA	mr1210	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
vg1006197301	3.09E-08	NA	mr1305	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
vg1006197301	7.29E-06	9.45E-06	mr1305	Jap_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
vg1006197301	NA	1.20E-07	mr1364	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
vg1006197301	NA	3.26E-07	mr1443	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
vg1006197301	NA	5.47E-06	mr1559	Jap_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
vg1006197301	2.76E-07	NA	mr1586	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
vg1006197301	NA	9.24E-07	mr1606	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
vg1006197301	NA	2.02E-06	mr1622	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
vg1006197301	4.05E-06	1.43E-19	mr1768	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
vg1006197301	NA	2.91E-06	mr1768	Jap_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
vg1006197301	2.39E-07	7.01E-31	mr1768_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
vg1006197301	NA	2.48E-08	mr1768_2	Jap_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