RiceVarMap2

Detailed information for vg1105974434:

Variant ID: vg1105974434 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 5974434

Reference Allele: C

Alternative Allele: T

Primary Allele: C

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGG[C/T]
TCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCACTAGCTAGCCATGGA

Reverse complement sequence

TCCATGGCTAGCTAGTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGA[G/A]
CCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCG

Allele Frequencies:

Search:

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	40.20%	0.20%	5.25%	54.40%	NA
All Indica	2759	29.90%	0.30%	3.62%	66.11%	NA
All Japonica	1512	62.20%	0.00%	8.40%	29.37%	NA
Aus	269	16.40%	0.00%	2.60%	81.04%	NA
Indica I	595	32.30%	0.30%	7.06%	60.34%	NA
Indica II	465	21.50%	0.60%	3.66%	74.19%	NA
Indica III	913	29.80%	0.30%	0.77%	69.11%	NA
Indica Intermediate	786	33.30%	0.10%	4.33%	62.21%	NA
Temperate Japonica	767	57.00%	0.00%	11.21%	31.81%	NA
Tropical Japonica	504	65.30%	0.00%	4.56%	30.16%	NA
Japonica Intermediate	241	72.60%	0.00%	7.47%	19.92%	NA
VI/Aromatic	96	39.60%	0.00%	12.50%	47.92%	NA
Intermediate	90	54.40%	0.00%	2.22%	43.33%	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
vg1105974434	C -> T	LOC_Os11g10840.1	missense_variant ; p.Leu39Phe; MODERATE	synonymous_codon	Average:33.674; most accessible tissue: Callus, score: 75.127	N	N	N	N
vg1105974434	C -> DEL	LOC_Os11g10840.1	N	frameshift_variant	Average:33.674; 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 vg1105974434:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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