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Detailed information for vg1001423491:

Variant ID: vg1001423491 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1423491
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTTGATTGGGAATGATATTCCTATGCTTGAATCCGTTAAGACATCGTTGAAAAATAGTTTTTCTGTGAAGGACTTAGGGGAAGCAGCATATATTCTGGG[C/T]
ATAAGGATCTATAGAGATAGATCAAAGAGGCTAATTGGATTAAGCCAGAGTACATACATTGACAAGGTGTTGAAGAGGTTCAACATGCAAGATTCTAAGA

Reverse complement sequence

TCTTAGAATCTTGCATGTTGAACCTCTTCAACACCTTGTCAATGTATGTACTCTGGCTTAATCCAATTAGCCTCTTTGATCTATCTCTATAGATCCTTAT[G/A]
CCCAGAATATATGCTGCTTCCCCTAAGTCCTTCACAGAAAAACTATTTTTCAACGATGTCTTAACGGATTCAAGCATAGGAATATCATTCCCAATCAACA

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%	20.50%	0.23%	2.14%	NA
All Indica	2759	94.90%	1.80%	0.25%	3.04%	NA
All Japonica	1512	45.60%	54.00%	0.20%	0.13%	NA
Aus	269	97.80%	0.00%	0.00%	2.23%	NA
Indica I	595	99.50%	0.30%	0.00%	0.17%	NA
Indica II	465	94.60%	3.00%	0.22%	2.15%	NA
Indica III	913	92.80%	0.40%	0.44%	6.35%	NA
Indica Intermediate	786	94.00%	3.80%	0.25%	1.91%	NA
Temperate Japonica	767	72.40%	27.20%	0.39%	0.00%	NA
Tropical Japonica	504	19.20%	80.80%	0.00%	0.00%	NA
Japonica Intermediate	241	15.80%	83.40%	0.00%	0.83%	NA
VI/Aromatic	96	12.50%	80.20%	0.00%	7.29%	NA
Intermediate	90	66.70%	30.00%	1.11%	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
vg1001423491	C -> T	LOC_Os10g03350.1	synonymous_variant ; p.Gly216Gly; LOW	synonymous_codon	Average:22.157; most accessible tissue: Zhenshan97 flower, score: 35.75	N	N	N	N
vg1001423491	C -> DEL	LOC_Os10g03350.1	N	frameshift_variant	Average:22.157; most accessible tissue: Zhenshan97 flower, score: 35.75	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001423491	NA	8.22E-06	mr1177	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
vg1001423491	NA	1.84E-08	mr1514	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
vg1001423491	NA	1.36E-07	mr1570	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
vg1001423491	1.46E-06	NA	mr1486_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
vg1001423491	4.28E-06	1.75E-10	mr1486_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