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Detailed information for vg1003750840:

Variant ID: vg1003750840 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3750840
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTTGCCCATAACCGAGGGTGTGGCTATTCGAATAGTTTTTAACTCTGATAAGAGGTGTACAACTTTACCCACAAGACACAACCTCAACACGTGTTGCCA[C/T]
GCACCGGGTATCACCACGGTACTCAGATAGAGGTCCTGACAAGACTATCCATCTAGGTCTACCCAAAACAGGAGAACCCGCTGAGGTTTCACCGCCCGCC

Reverse complement sequence

GGCGGGCGGTGAAACCTCAGCGGGTTCTCCTGTTTTGGGTAGACCTAGATGGATAGTCTTGTCAGGACCTCTATCTGAGTACCGTGGTGATACCCGGTGC[G/A]
TGGCAACACGTGTTGAGGTTGTGTCTTGTGGGTAAAGTTGTACACCTCTTATCAGAGTTAAAAACTATTCGAATAGCCACACCCTCGGTTATGGGCAAGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.40%	5.70%	2.18%	15.70%	NA
All Indica	2759	67.30%	3.30%	3.44%	25.99%	NA
All Japonica	1512	89.50%	10.40%	0.00%	0.07%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	83.90%	0.00%	1.51%	14.62%	NA
Indica II	465	74.40%	1.70%	2.15%	21.72%	NA
Indica III	913	44.10%	7.10%	6.02%	42.72%	NA
Indica Intermediate	786	77.40%	2.30%	2.67%	17.68%	NA
Temperate Japonica	767	91.00%	8.90%	0.00%	0.13%	NA
Tropical Japonica	504	86.10%	13.90%	0.00%	0.00%	NA
Japonica Intermediate	241	91.70%	8.30%	0.00%	0.00%	NA
VI/Aromatic	96	56.20%	19.80%	3.12%	20.83%	NA
Intermediate	90	88.90%	3.30%	3.33%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003750840	C -> T	LOC_Os10g07150.1	3_prime_UTR_variant ; 737.0bp to feature; MODIFIER	silent_mutation	Average:24.282; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N
vg1003750840	C -> T	LOC_Os10g07130.1	upstream_gene_variant ; 4691.0bp to feature; MODIFIER	silent_mutation	Average:24.282; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N
vg1003750840	C -> T	LOC_Os10g07160.1	downstream_gene_variant ; 4267.0bp to feature; MODIFIER	silent_mutation	Average:24.282; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N
vg1003750840	C -> T	LOC_Os10g07150.2	intron_variant ; MODIFIER	silent_mutation	Average:24.282; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N
vg1003750840	C -> DEL	N	N	silent_mutation	Average:24.282; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003750840	NA	7.95E-06	mr1415_2	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
vg1003750840	NA	2.59E-06	mr1415_2	Jap_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
vg1003750840	NA	6.86E-07	mr1559_2	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
vg1003750840	NA	6.45E-07	mr1559_2	Jap_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
vg1003750840	4.09E-09	5.77E-11	mr1748_2	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