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Detailed information for vg0507601642:

Variant ID: vg0507601642 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7601642
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCGCCATCGACTTCGCCAGGTGATCTATCTCCACCGGAGTTCACCGAGAACGAGAAAACCCTTCGTGGAGGAACTCGAGGTGCAGTTGCGGACGATGAT[G/C]
TCGTATGCAAGCCAACACGTGCCCTCCGGCATATCGGCTCGATCGACGGCACTCCTGCTTCAGGGCTTCGTCGATACGCTTTGAAGCATCTAGGCCCCCG

Reverse complement sequence

CGGGGGCCTAGATGCTTCAAAGCGTATCGACGAAGCCCTGAAGCAGGAGTGCCGTCGATCGAGCCGATATGCCGGAGGGCACGTGTTGGCTTGCATACGA[C/G]
ATCATCGTCCGCAACTGCACCTCGAGTTCCTCCACGAAGGGTTTTCTCGTTCTCGGTGAACTCCGGTGGAGATAGATCACCTGGCGAAGTCGATGGCGCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.20%	2.40%	7.13%	35.27%	NA
All Indica	2759	34.30%	0.10%	7.54%	58.06%	NA
All Japonica	1512	84.20%	7.20%	7.67%	0.93%	NA
Aus	269	84.40%	0.40%	3.35%	11.90%	NA
Indica I	595	24.50%	0.20%	5.55%	69.75%	NA
Indica II	465	39.10%	0.00%	9.68%	51.18%	NA
Indica III	913	34.60%	0.10%	9.09%	56.19%	NA
Indica Intermediate	786	38.30%	0.30%	5.98%	55.47%	NA
Temperate Japonica	767	72.80%	13.00%	12.91%	1.30%	NA
Tropical Japonica	504	98.00%	0.20%	1.19%	0.60%	NA
Japonica Intermediate	241	91.70%	3.30%	4.56%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	74.40%	0.00%	4.44%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507601642	G -> DEL	N	N	silent_mutation	Average:13.879; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0507601642	G -> C	LOC_Os05g13730.1	upstream_gene_variant ; 1741.0bp to feature; MODIFIER	silent_mutation	Average:13.879; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0507601642	G -> C	LOC_Os05g13710.1	downstream_gene_variant ; 4868.0bp to feature; MODIFIER	silent_mutation	Average:13.879; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0507601642	G -> C	LOC_Os05g13720.1	downstream_gene_variant ; 1067.0bp to feature; MODIFIER	silent_mutation	Average:13.879; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0507601642	G -> C	LOC_Os05g13720-LOC_Os05g13730	intergenic_region ; MODIFIER	silent_mutation	Average:13.879; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507601642	3.54E-08	5.80E-10	mr1588_2	Jap_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