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Detailed information for vg0320729993:

Variant ID: vg0320729993 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20729993
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGACATCTAGCTTCGTCGACAACAGCGTCAACACCAACTGCAACCAAGGAGTTCTCACTTCAACAACGCTGGTGTGGACTCAAGTCGGCGAAATCGTCTT[T/C]
CTGGTTTACACCACAGTGCCGATCTCAGCTGGTCCGCCAATGGCCGGAAACGAGAACGCAGTGGCTACAACCCAGGACGACTCCATGTCGAAGGATCCTC

Reverse complement sequence

GAGGATCCTTCGACATGGAGTCGTCCTGGGTTGTAGCCACTGCGTTCTCGTTTCCGGCCATTGGCGGACCAGCTGAGATCGGCACTGTGGTGTAAACCAG[A/G]
AAGACGATTTCGCCGACTTGAGTCCACACCAGCGTTGTTGAAGTGAGAACTCCTTGGTTGCAGTTGGTGTTGACGCTGTTGTCGACGAAGCTAGATGTCA

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	96.50%	1.10%	2.39%	0.00%	NA
All Indica	2759	97.60%	0.90%	1.56%	0.00%	NA
All Japonica	1512	96.40%	0.70%	2.98%	0.00%	NA
Aus	269	86.60%	4.80%	8.55%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	92.70%	2.20%	5.16%	0.00%	NA
Indica III	913	99.00%	0.50%	0.44%	0.00%	NA
Indica Intermediate	786	97.20%	0.90%	1.91%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	89.90%	2.00%	8.13%	0.00%	NA
Japonica Intermediate	241	98.30%	0.00%	1.66%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	95.60%	3.30%	1.11%	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
vg0320729993	T -> C	LOC_Os03g37411.1	intron_variant ; MODIFIER	silent_mutation	Average:30.727; most accessible tissue: Zhenshan97 panicle, score: 81.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320729993	4.29E-06	NA	mr1130	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