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Detailed information for vg0230849830:

Variant ID: vg0230849830 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 30849830
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCGTGGAAGCTGCCGGAAGGCAGAGCCCCCGAGATGGTGGCTGTAGTCGTGGGCCAGGCGACGAAGCGCAGTCCAGGAGAGGTCCTGGTACGCGATCTG[G/A]
AGAGTGGGCCTGGCCACAGAGAAGTGGTGTGGGCGAAGGCCAGCTCCGTGTATACCTCCACGAGGGTAAAGGTACACAGAGAGCTCACAGCGAGGGGGAA

Reverse complement sequence

TTCCCCCTCGCTGTGAGCTCTCTGTGTACCTTTACCCTCGTGGAGGTATACACGGAGCTGGCCTTCGCCCACACCACTTCTCTGTGGCCAGGCCCACTCT[C/T]
CAGATCGCGTACCAGGACCTCTCCTGGACTGCGCTTCGTCGCCTGGCCCACGACTACAGCCACCATCTCGGGGGCTCTGCCTTCCGGCAGCTTCCACGCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.60%	1.60%	3.75%	34.13%	NA
All Indica	2759	36.00%	1.80%	5.29%	56.98%	NA
All Japonica	1512	99.90%	0.00%	0.00%	0.13%	NA
Aus	269	70.60%	8.90%	11.52%	8.92%	NA
Indica I	595	17.80%	0.20%	4.54%	77.48%	NA
Indica II	465	41.50%	3.40%	6.45%	48.60%	NA
Indica III	913	40.60%	1.50%	5.26%	52.57%	NA
Indica Intermediate	786	41.00%	2.30%	5.22%	51.53%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	83.30%	1.10%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0230849830	G -> A	LOC_Os02g50510.1	synonymous_variant ; p.Leu76Leu; LOW	synonymous_codon	Average:16.095; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0230849830	G -> DEL	LOC_Os02g50510.1	N	frameshift_variant	Average:16.095; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0230849830	2.15E-06	1.25E-06	mr1310	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