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Detailed information for vg0714431042:

Variant ID: vg0714431042 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14431042
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTCTTTTGTGGGAAACGATCTTGTCTTGAATTAGATGAATGATTCTGTACTGACCTAGGTGATTCCTTCCACTCTTGATAATACGGCATAGGTGGTTGA[T/G]
GCATCCACGGCATGTAATACATAAAAGGATAACCAAACGGTGACATTGGATATGGATACCATGGCATCACAACCGGTGGTTTATATGGAGTTGGTATAGT

Reverse complement sequence

ACTATACCAACTCCATATAAACCACCGGTTGTGATGCCATGGTATCCATATCCAATGTCACCGTTTGGTTATCCTTTTATGTATTACATGCCGTGGATGC[A/C]
TCAACCACCTATGCCGTATTATCAAGAGTGGAAGGAATCACCTAGGTCAGTACAGAATCATTCATCTAATTCAAGACAAGATCGTTTCCCACAAAAGAAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.80%	1.70%	41.28%	10.26%	NA
All Indica	2759	27.00%	2.30%	59.04%	11.63%	NA
All Japonica	1512	83.70%	0.70%	6.48%	9.06%	NA
Aus	269	21.20%	1.90%	70.26%	6.69%	NA
Indica I	595	52.60%	1.00%	25.21%	21.18%	NA
Indica II	465	32.00%	2.60%	58.71%	6.67%	NA
Indica III	913	3.40%	2.80%	85.21%	8.54%	NA
Indica Intermediate	786	32.20%	2.40%	54.45%	10.94%	NA
Temperate Japonica	767	84.50%	0.40%	3.00%	12.13%	NA
Tropical Japonica	504	93.70%	0.20%	5.16%	0.99%	NA
Japonica Intermediate	241	60.60%	2.90%	20.33%	16.18%	NA
VI/Aromatic	96	83.30%	0.00%	13.54%	3.12%	NA
Intermediate	90	68.90%	0.00%	24.44%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714431042	T -> DEL	LOC_Os07g25260.1	N	frameshift_variant	Average:9.47; most accessible tissue: Callus, score: 26.138	N	N	N	N
vg0714431042	T -> G	LOC_Os07g25260.1	missense_variant ; p.His177Pro; MODERATE	nonsynonymous_codon ; H177P	Average:9.47; most accessible tissue: Callus, score: 26.138	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714431042	2.08E-06	9.95E-07	mr1134	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
vg0714431042	2.42E-06	1.70E-06	mr1135	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