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Detailed information for vg0421298734:

Variant ID: vg0421298734 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21298734
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCCTCCATTAATGGGCGGAGATTTGCAATGGCCGCTGTCCGAATGACCCTCCGATGGGATGGGTCATACCTACTTCCACTCCGCCGGAAGCAGATGCAA[T/C]
GTGGGAGCACGGTTGTCTGCCGATGACGTAACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGCGTCAGTTTAGCATGCCGCACGTCT

Reverse complement sequence

AGACGTGCGGCATGCTAAACTGACGCGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTTACGTCATCGGCAGACAACCGTGCTCCCAC[A/G]
TTGCATCTGCTTCCGGCGGAGTGGAAGTAGGTATGACCCATCCCATCGGAGGGTCATTCGGACAGCGGCCATTGCAAATCTCCGCCCATTAATGGAGGAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.10%	0.40%	0.17%	5.35%	NA
All Indica	2759	99.20%	0.70%	0.14%	0.04%	NA
All Japonica	1512	84.30%	0.00%	0.26%	15.48%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.90%	0.40%	0.43%	0.22%	NA
Indica III	913	99.00%	0.90%	0.11%	0.00%	NA
Indica Intermediate	786	99.10%	0.80%	0.13%	0.00%	NA
Temperate Japonica	767	88.30%	0.00%	0.00%	11.73%	NA
Tropical Japonica	504	88.30%	0.00%	0.40%	11.31%	NA
Japonica Intermediate	241	63.10%	0.00%	0.83%	36.10%	NA
VI/Aromatic	96	84.40%	1.00%	0.00%	14.58%	NA
Intermediate	90	96.70%	0.00%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0421298734	T -> C	LOC_Os04g35050.1	upstream_gene_variant ; 670.0bp to feature; MODIFIER	silent_mutation	Average:17.124; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0421298734	T -> C	LOC_Os04g35030-LOC_Os04g35050	intergenic_region ; MODIFIER	silent_mutation	Average:17.124; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0421298734	T -> DEL	N	N	silent_mutation	Average:17.124; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421298734	NA	8.89E-06	mr1169_2	Ind_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
vg0421298734	5.50E-06	5.90E-06	mr1827_2	Ind_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
vg0421298734	2.22E-06	NA	mr1902_2	Ind_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