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Detailed information for vg1008388235:

Variant ID: vg1008388235 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 8388235
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TCCACAACAGTTTAAGATCTTCGACCAGTGGTCTTAGGTACACATCGATGTCGTTATCAGGTTGCTTGGGGCCTTGAAGAATAATCGGCATCATTATGTA[C/T]
TTCCTCTTCATGCATAGCCAAGGAGGGAGGTTGTAGATACACATCGTAACGGGCCAAGTGCTATGGCCGCTGCTCATCTCTCCAAAAGGATTCATGCCAT

Reverse complement sequence

ATGGCATGAATCCTTTTGGAGAGATGAGCAGCGGCCATAGCACTTGGCCCGTTACGATGTGTATCTACAACCTCCCTCCTTGGCTATGCATGAAGAGGAA[G/A]
TACATAATGATGCCGATTATTCTTCAAGGCCCCAAGCAACCTGATAACGACATCGATGTGTACCTAAGACCACTGGTCGAAGATCTTAAACTGTTGTGGA

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	78.80%	21.10%	0.06%	0.00%	NA
All Indica	2759	64.70%	35.20%	0.11%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	90.60%	9.20%	0.17%	0.00%	NA
Indica II	465	41.10%	58.70%	0.22%	0.00%	NA
Indica III	913	64.20%	35.70%	0.11%	0.00%	NA
Indica Intermediate	786	59.80%	40.20%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg1008388235	C -> T	LOC_Os10g16840.1	synonymous_variant ; p.Lys321Lys; LOW	synonymous_codon	Average:25.751; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1008388235	NA	4.24E-11	mr1709	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
vg1008388235	NA	1.33E-08	mr1709	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
vg1008388235	2.36E-06	NA	mr1027_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
vg1008388235	8.83E-08	1.86E-11	mr1027_2	Ind_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
vg1008388235	NA	6.03E-07	mr1057_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
vg1008388235	NA	5.23E-08	mr1057_2	Ind_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
vg1008388235	NA	1.83E-06	mr1551_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
vg1008388235	NA	2.07E-06	mr1580_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
vg1008388235	NA	2.68E-09	mr1649_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
vg1008388235	NA	2.19E-10	mr1709_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
vg1008388235	NA	7.41E-09	mr1709_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
vg1008388235	NA	2.75E-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
vg1008388235	7.96E-06	7.96E-06	mr1939_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