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Detailed information for vg0518095913:

Variant ID: vg0518095913 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 18095913
Reference Allele: T	Alternative Allele: C,G
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGGCAAAGCACAATTTGATACCCATGTCGTCACAGTAATCGCCAAACAGCTCACTAGTGAACTGGGTGCCGTTGTCTGTAATGATACGGTTGGGCACTC[T/C,G]
GAATCAAGACGTGGTGCCCCTGATGAACTTAAGAGCAGAATGCTTGTCGATTTTGACAACTGGGTAGGCCTCGGGCCACTTGGTGAATTTGTCGATGGCG

Reverse complement sequence

CGCCATCGACAAATTCACCAAGTGGCCCGAGGCCTACCCAGTTGTCAAAATCGACAAGCATTCTGCTCTTAAGTTCATCAGGGGCACCACGTCTTGATTC[A/G,C]
GAGTGCCCAACCGTATCATTACAGACAACGGCACCCAGTTCACTAGTGAGCTGTTTGGCGATTACTGTGACGACATGGGTATCAAATTGTGCTTTGCCTC

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	81.40%	14.20%	3.28%	1.10%	G: 0.02%
All Indica	2759	98.90%	0.50%	0.47%	0.07%	G: 0.04%
All Japonica	1512	57.50%	42.30%	0.20%	0.00%	NA
Aus	269	33.10%	0.00%	49.07%	17.84%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	97.20%	1.90%	0.86%	0.00%	NA
Indica III	913	99.10%	0.30%	0.44%	0.00%	G: 0.11%
Indica Intermediate	786	98.90%	0.40%	0.51%	0.25%	NA
Temperate Japonica	767	24.50%	75.40%	0.13%	0.00%	NA
Tropical Japonica	504	98.00%	2.00%	0.00%	0.00%	NA
Japonica Intermediate	241	78.00%	21.20%	0.83%	0.00%	NA
VI/Aromatic	96	92.70%	1.00%	5.21%	1.04%	NA
Intermediate	90	80.00%	16.70%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0518095913	T -> DEL	LOC_Os05g31120.1	N	frameshift_variant	Average:45.386; most accessible tissue: Zhenshan97 flag leaf, score: 67.785	N	N	N	N
vg0518095913	T -> G	LOC_Os05g31120.1	synonymous_variant ; p.Ser325Ser; LOW	synonymous_codon	Average:45.386; most accessible tissue: Zhenshan97 flag leaf, score: 67.785	N	N	N	N
vg0518095913	T -> C	LOC_Os05g31120.1	synonymous_variant ; p.Ser325Ser; LOW	synonymous_codon	Average:45.386; most accessible tissue: Zhenshan97 flag leaf, score: 67.785	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0518095913	NA	2.37E-07	mr1129	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
vg0518095913	NA	6.96E-07	mr1543	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
vg0518095913	NA	1.29E-11	mr1879	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
vg0518095913	NA	1.52E-06	mr1880	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
vg0518095913	1.83E-07	NA	mr1758_2	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
vg0518095913	NA	1.27E-07	mr1952_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
vg0518095913	NA	4.69E-08	mr1952_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
vg0518095913	NA	1.63E-06	mr1966_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