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Detailed information for vg0819075122:

Variant ID: vg0819075122 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19075122
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTATCACTTTTTCTATTGTAAATTTGGTACCTAGGTACTATGAGGTATCATGAGGTAACAAAAAAAATAATGTAAAATTTGGTACCTCATTGTACCTCCT[T/C]
AAGGACCGTAAAATTGCTCTAAAGTTTATGGTTTGAAACTAAAATAGTCAAAATAATTATGAAATAGGGAAGCTGGATTATCAAAATTCCTTTCTACCGT

Reverse complement sequence

ACGGTAGAAAGGAATTTTGATAATCCAGCTTCCCTATTTCATAATTATTTTGACTATTTTAGTTTCAAACCATAAACTTTAGAGCAATTTTACGGTCCTT[A/G]
AGGAGGTACAATGAGGTACCAAATTTTACATTATTTTTTTTGTTACCTCATGATACCTCATAGTACCTAGGTACCAAATTTACAATAGAAAAAGTGATAC

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	85.10%	13.20%	1.42%	0.28%	NA
All Indica	2759	98.30%	1.10%	0.14%	0.47%	NA
All Japonica	1512	61.40%	34.50%	4.10%	0.00%	NA
Aus	269	94.10%	5.90%	0.00%	0.00%	NA
Indica I	595	96.80%	2.70%	0.50%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	97.90%	0.70%	0.00%	1.42%	NA
Indica Intermediate	786	99.00%	0.90%	0.13%	0.00%	NA
Temperate Japonica	767	36.20%	58.80%	4.95%	0.00%	NA
Tropical Japonica	504	94.80%	3.60%	1.59%	0.00%	NA
Japonica Intermediate	241	71.40%	22.00%	6.64%	0.00%	NA
VI/Aromatic	96	63.50%	35.40%	1.04%	0.00%	NA
Intermediate	90	76.70%	23.30%	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
vg0819075122	T -> C	LOC_Os08g30900.1	intron_variant ; MODIFIER	silent_mutation	Average:43.482; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0819075122	T -> C	LOC_Os08g30900.2	intron_variant ; MODIFIER	silent_mutation	Average:43.482; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0819075122	T -> DEL	N	N	silent_mutation	Average:43.482; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819075122	7.90E-06	NA	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
vg0819075122	NA	1.20E-08	mr1182_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
vg0819075122	3.00E-07	NA	mr1261_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
vg0819075122	NA	5.08E-10	mr1282_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
vg0819075122	NA	4.06E-07	mr1282_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
vg0819075122	NA	1.65E-06	mr1330_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
vg0819075122	NA	5.91E-10	mr1530_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
vg0819075122	8.72E-07	4.76E-18	mr1980_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
vg0819075122	NA	8.38E-08	mr1980_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