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Detailed information for vg1127487577:

Variant ID: vg1127487577 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27487577
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTACTTGGAGGTTGAGGTTGTTTCAGGTAGGGAGATGAAGGTGATTTGGGGGTTCTTCACTGGCATCATGGAGGAGGAAGAAGGTGGTGATCAAGAGGA[G/C]
GTGTTGCTTGAGGAGAAGAAAATGTTGGTTGATGTTGTGGGCTTCTCTACCTCCTTGGAGTTCCTCCAACATCATCTCTCACATTGTTGCAAGGTATAAT

Reverse complement sequence

ATTATACCTTGCAACAATGTGAGAGATGATGTTGGAGGAACTCCAAGGAGGTAGAGAAGCCCACAACATCAACCAACATTTTCTTCTCCTCAAGCAACAC[C/G]
TCCTCTTGATCACCACCTTCTTCCTCCTCCATGATGCCAGTGAAGAACCCCCAAATCACCTTCATCTCCCTACCTGAAACAACCTCAACCTCCAAGTACT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.40%	15.30%	0.28%	0.00%	NA
All Indica	2759	84.00%	15.70%	0.25%	0.00%	NA
All Japonica	1512	86.80%	13.10%	0.13%	0.00%	NA
Aus	269	95.50%	4.10%	0.37%	0.00%	NA
Indica I	595	89.10%	10.90%	0.00%	0.00%	NA
Indica II	465	96.30%	3.40%	0.22%	0.00%	NA
Indica III	913	73.40%	26.20%	0.44%	0.00%	NA
Indica Intermediate	786	85.20%	14.50%	0.25%	0.00%	NA
Temperate Japonica	767	98.00%	2.00%	0.00%	0.00%	NA
Tropical Japonica	504	70.40%	29.60%	0.00%	0.00%	NA
Japonica Intermediate	241	85.10%	14.10%	0.83%	0.00%	NA
VI/Aromatic	96	30.20%	67.70%	2.08%	0.00%	NA
Intermediate	90	82.20%	16.70%	1.11%	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
vg1127487577	G -> C	LOC_Os11g45400.1	missense_variant ; p.Glu204Asp; MODERATE	nonsynonymous_codon ; E204D	Average:51.941; most accessible tissue: Zhenshan97 young leaf, score: 75.397	unknown	unknown	TOLERATED	0.38

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127487577	NA	2.04E-06	mr1448	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
vg1127487577	NA	5.68E-11	mr1125_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
vg1127487577	NA	9.47E-07	mr1798_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