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Detailed information for vg0402601495:

Variant ID: vg0402601495 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2601495
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGATTGCGGCTTCGGTCCCAGTTAACTCCGGAAGCGTCCGCACGTCGAGTGGCAGCTGAGTCCCCCATCTTCGATCTCACGACTACCACCAGCCAAGCCT[T/C]
AGCATCACTGGCGCAGGATCTAATCGCAGGAGCAGGGGTCACGACGAGTGATCTGTCCACTCGCCTCCCGACCATCATAGGGAGCGCCGAGTGGAATGAC

Reverse complement sequence

GTCATTCCACTCGGCGCTCCCTATGATGGTCGGGAGGCGAGTGGACAGATCACTCGTCGTGACCCCTGCTCCTGCGATTAGATCCTGCGCCAGTGATGCT[A/G]
AGGCTTGGCTGGTGGTAGTCGTGAGATCGAAGATGGGGGACTCAGCTGCCACTCGACGTGCGGACGCTTCCGGAGTTAACTGGGACCGAAGCCGCAATCA

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	76.70%	7.20%	3.20%	12.95%	NA
All Indica	2759	78.10%	9.60%	3.59%	8.66%	NA
All Japonica	1512	72.60%	1.90%	3.04%	22.49%	NA
Aus	269	77.70%	11.50%	1.86%	8.92%	NA
Indica I	595	97.30%	2.40%	0.00%	0.34%	NA
Indica II	465	85.20%	4.30%	4.73%	5.81%	NA
Indica III	913	62.10%	17.30%	4.60%	15.99%	NA
Indica Intermediate	786	78.00%	9.40%	4.45%	8.14%	NA
Temperate Japonica	767	91.50%	0.70%	0.65%	7.17%	NA
Tropical Japonica	504	48.80%	2.20%	6.15%	42.86%	NA
Japonica Intermediate	241	61.80%	5.40%	4.15%	28.63%	NA
VI/Aromatic	96	94.80%	3.10%	0.00%	2.08%	NA
Intermediate	90	81.10%	10.00%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402601495	T -> C	LOC_Os04g05220.1	upstream_gene_variant ; 2332.0bp to feature; MODIFIER	silent_mutation	Average:24.205; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0402601495	T -> C	LOC_Os04g05200.1	downstream_gene_variant ; 4782.0bp to feature; MODIFIER	silent_mutation	Average:24.205; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0402601495	T -> C	LOC_Os04g05210.1	intron_variant ; MODIFIER	silent_mutation	Average:24.205; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0402601495	T -> DEL	N	N	silent_mutation	Average:24.205; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402601495	7.64E-06	NA	mr1307	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
vg0402601495	2.04E-06	2.04E-06	mr1307	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