RiceVarMap2

Detailed information for vg1105974479:

Variant ID: vg1105974479 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 5974479

Reference Allele: G

Alternative Allele: A

Primary Allele: G

Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTC[G/A]
CCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCACTAGCTAGCCATGGACAGAAAACGCACGCGACTGCTGCATATATGCATGGCTGCATCATC

Reverse complement sequence

GATGATGCAGCCATGCATATATGCAGCAGTCGCGTGCGTTTTCTGTCCATGGCTAGCTAGTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGG[C/T]
GAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.90%	2.60%	0.76%	47.65%	NA
All Indica	2759	34.40%	0.80%	1.01%	63.79%	NA
All Japonica	1512	77.40%	6.60%	0.20%	15.74%	NA
Aus	269	19.00%	0.00%	1.86%	79.18%	NA
Indica I	595	42.50%	0.00%	0.17%	57.31%	NA
Indica II	465	27.10%	0.20%	1.08%	71.61%	NA
Indica III	913	29.10%	1.80%	0.99%	68.13%	NA
Indica Intermediate	786	38.70%	0.60%	1.65%	59.03%	NA
Temperate Japonica	767	72.40%	2.10%	0.39%	25.16%	NA
Tropical Japonica	504	83.10%	13.30%	0.00%	3.57%	NA
Japonica Intermediate	241	81.70%	7.10%	0.00%	11.20%	NA
VI/Aromatic	96	88.50%	0.00%	0.00%	11.46%	NA
Intermediate	90	63.30%	3.30%	0.00%	33.33%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105974479	G -> A	LOC_Os11g10840.1	missense_variant ; p.Ala54Thr; MODERATE	nonsynonymous_codon ; A54T	Average:38.814; most accessible tissue: Callus, score: 75.127	possibly damaging	1.571	TOLERATED	0.11
vg1105974479	G -> DEL	LOC_Os11g10840.1	N	frameshift_variant	Average:38.814; most accessible tissue: Callus, score: 75.127	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg1105974479:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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