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Detailed information for vg0705191402:

Variant ID: vg0705191402 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 5191402
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTGCTCTGATCGAGGAGCTCGTTCTTCCTCCTGCAGCAATGGTGAACCATCACGATGACTCTGTCTCTGACATCGCCGATCATGGCTGCTCCGGCGCCG[C/T]
TCCTCCTCCTTCAGCAGTGGTGGACCTCCCCGATGACTCTGACGGCGCCGATCAGAGCTGCTCCGGCATGGTGGATGATTCCCTTCCCGGGTACTATGAG

Reverse complement sequence

CTCATAGTACCCGGGAAGGGAATCATCCACCATGCCGGAGCAGCTCTGATCGGCGCCGTCAGAGTCATCGGGGAGGTCCACCACTGCTGAAGGAGGAGGA[G/A]
CGGCGCCGGAGCAGCCATGATCGGCGATGTCAGAGACAGAGTCATCGTGATGGTTCACCATTGCTGCAGGAGGAAGAACGAGCTCCTCGATCAGAGCAGT

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	52.10%	47.80%	0.04%	0.08%	NA
All Indica	2759	76.80%	23.00%	0.07%	0.14%	NA
All Japonica	1512	2.70%	97.30%	0.00%	0.00%	NA
Aus	269	96.30%	3.70%	0.00%	0.00%	NA
Indica I	595	97.30%	2.70%	0.00%	0.00%	NA
Indica II	465	89.50%	10.10%	0.22%	0.22%	NA
Indica III	913	57.10%	42.70%	0.00%	0.22%	NA
Indica Intermediate	786	76.70%	23.00%	0.13%	0.13%	NA
Temperate Japonica	767	4.70%	95.30%	0.00%	0.00%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	42.20%	57.80%	0.00%	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
vg0705191402	C -> DEL	LOC_Os07g09740.1	N	frameshift_variant	Average:58.679; most accessible tissue: Minghui63 flag leaf, score: 74.955	N	N	N	N
vg0705191402	C -> T	LOC_Os07g09740.1	missense_variant ; p.Ala533Val; MODERATE	nonsynonymous_codon ; A533V	Average:58.679; most accessible tissue: Minghui63 flag leaf, score: 74.955	benign	-1.069	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0705191402	NA	4.79E-27	mr1072	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
vg0705191402	NA	5.13E-06	mr1072	Ind_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
vg0705191402	NA	7.50E-06	mr1075	Ind_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
vg0705191402	NA	1.17E-06	mr1124	Ind_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
vg0705191402	NA	3.81E-28	mr1723	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
vg0705191402	NA	9.32E-06	mr1870	Ind_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
vg0705191402	NA	5.45E-27	mr1074_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
vg0705191402	NA	1.54E-09	mr1124_2	Ind_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
vg0705191402	NA	9.20E-19	mr1239_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
vg0705191402	1.36E-08	1.61E-09	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
vg0705191402	NA	2.11E-09	mr1600_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
vg0705191402	NA	1.11E-32	mr1723_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