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Detailed information for vg1119005779:

Variant ID: vg1119005779 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 19005779
Reference Allele: ATGG	Alternative Allele: GTGG,A
Primary Allele: ATGG	Secondary Allele: GTGG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACCCTTGGCAATGGTGGCACTGAATGCGTCCCGTCGAGGCGACAGATGAGGCACTCTTGGCGGGTACCTGCGAGGAACTTTTACCTGACTCTGCTGGTC[ATGG/GTGG,A]
TGGAGATGGTTTTGGTGCCGCAGAAGCTCCGGATGCAGCTGGTCACTTGCTCGCTAGCTGGGAGGATGCCCGAAAAGAGACGGCCTTGGGCAGTCCCGCA

Reverse complement sequence

TGCGGGACTGCCCAAGGCCGTCTCTTTTCGGGCATCCTCCCAGCTAGCGAGCAAGTGACCAGCTGCATCCGGAGCTTCTGCGGCACCAAAACCATCTCCA[CCAT/CCAC,T]
GACCAGCAGAGTCAGGTAAAAGTTCCTCGCAGGTACCCGCCAAGAGTGCCTCATCTGTCGCCTCGACGGGACGCATTCAGTGCCACCATTGCCAAGGGTT

Allele Frequencies:

Populations	Population Size	Frequency of ATGG(primary allele)	Frequency of GTGG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.20%	34.30%	4.46%	20.08%	NA
All Indica	2759	49.80%	43.10%	2.83%	4.31%	NA
All Japonica	1512	32.80%	6.50%	7.94%	52.78%	NA
Aus	269	5.20%	94.40%	0.37%	0.00%	NA
Indica I	595	26.90%	71.80%	0.17%	1.18%	NA
Indica II	465	65.40%	26.90%	2.58%	5.16%	NA
Indica III	913	53.80%	36.80%	4.27%	5.15%	NA
Indica Intermediate	786	53.30%	38.20%	3.31%	5.22%	NA
Temperate Japonica	767	49.70%	4.80%	3.52%	41.98%	NA
Tropical Japonica	504	10.10%	9.70%	15.87%	64.29%	NA
Japonica Intermediate	241	26.60%	5.00%	5.39%	63.07%	NA
VI/Aromatic	96	22.90%	49.00%	6.25%	21.88%	NA
Intermediate	90	43.30%	37.80%	6.67%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119005779	ATGG -> GTGG	LOC_Os11g32180.1	intron_variant ; MODIFIER	silent_mutation	Average:32.787; most accessible tissue: Zhenshan97 flower, score: 71.382	N	N	N	N
vg1119005779	ATGG -> A	LOC_Os11g32180.1	intron_variant ; MODIFIER	N	Average:32.787; most accessible tissue: Zhenshan97 flower, score: 71.382	N	N	N	N
vg1119005779	ATGG -> DEL	N	N	silent_mutation	Average:32.787; most accessible tissue: Zhenshan97 flower, score: 71.382	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119005779	1.79E-06	4.42E-06	mr1865_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