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Detailed information for vg0311212518:

Variant ID: vg0311212518 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 11212518
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

ATTATTCTTGAACTATGGTGGTGTGGAGAATTTCCTATTAATACACTTTCCATTTATCTAACTGCGCTGTAAATTCTAAAGTCATATGATACTCTTTGGT[C/T]
TGACGCAGTTTTAACTTTTTTTTACAGATTGAGCCACATGACTATATCTCGAAGCTCTTCAATCTATTTGTTCAGTTTAACAATGTCTTGACTGATTTCG

Reverse complement sequence

CGAAATCAGTCAAGACATTGTTAAACTGAACAAATAGATTGAAGAGCTTCGAGATATAGTCATGTGGCTCAATCTGTAAAAAAAAGTTAAAACTGCGTCA[G/A]
ACCAAAGAGTATCATATGACTTTAGAATTTACAGCGCAGTTAGATAAATGGAAAGTGTATTAATAGGAAATTCTCCACACCACCATAGTTCAAGAATAAT

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	97.00%	1.80%	1.14%	0.00%	NA
All Indica	2759	98.90%	0.10%	1.01%	0.00%	NA
All Japonica	1512	93.20%	5.40%	1.46%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.00%	0.00%	3.03%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.60%	0.30%	1.15%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	82.90%	13.50%	3.57%	0.00%	NA
Japonica Intermediate	241	93.80%	5.00%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	3.30%	4.44%	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
vg0311212518	C -> T	LOC_Os03g19930.1	intron_variant ; MODIFIER	silent_mutation	Average:53.617; most accessible tissue: Callus, score: 83.554	N	N	N	N
vg0311212518	C -> T	LOC_Os03g19930.2	intron_variant ; MODIFIER	silent_mutation	Average:53.617; most accessible tissue: Callus, score: 83.554	N	N	N	N
vg0311212518	C -> T	LOC_Os03g19930.3	intron_variant ; MODIFIER	silent_mutation	Average:53.617; most accessible tissue: Callus, score: 83.554	N	N	N	N
vg0311212518	C -> T	LOC_Os03g19930.4	intron_variant ; MODIFIER	silent_mutation	Average:53.617; most accessible tissue: Callus, score: 83.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0311212518	NA	1.08E-06	mr1156	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
vg0311212518	NA	2.64E-06	mr1179	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
vg0311212518	NA	6.99E-09	mr1422_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
vg0311212518	NA	1.22E-06	mr1583_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
vg0311212518	4.93E-09	1.54E-10	mr1850_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